https://www.na-mic.org/w/api.php?action=feedcontributions&user=Ivo&feedformat=atomNAMIC Wiki - User contributions [en]2024-03-28T13:11:41ZUser contributionsMediaWiki 1.33.0https://www.na-mic.org/w/index.php?title=SDIWG:Meeting_Minutes_20100528&diff=53112SDIWG:Meeting Minutes 201005282010-05-28T19:12:18Z<p>Ivo: /* Minutes */</p>
<hr />
<div>==NCBC Joint Working Group Meeting==<br />
<br />
[[SDIWG:Software_and_Data_Integration_Working_Group|Top page of SDIWG web site]]<br />
<br />
===Notes===<br />
''Friday May 28, 2010: 2:30-3:30 PM EST''<br><br />
''Please contact Peter Lyster for information [mailto:lysterp@mail.nih.gov Peter Lyster]''<br><br />
''[[SDIWG:Software_Engineering_Body_of_Knowledge_Across_NCBC_Biocomputing_Centers | SDIWG Meetings Page]]''<br><br />
<b>Save the date for the next SDWIG tcon/Connect, three months from now: August 20, 2010</b><br />
<br />
===Tcon DRAFT Agenda===<br />
<br />
*Roll Call/Note-taker (Ivo) (5 min)<br />
*Minutes from the last SDIWG tcon [[SDIWG:Meeting_Minutes_20100219|February 19, 2010]] (5 min)<br />
*Status check on '''working groups''': <br />
**[http://www.biositemaps.org Biositemaps] is a technology to address (i) describing, (ii) locating, (ii) querying, (iii) composing or combining, and (iv) navigating/mining biomedical resources. The underlying technology for Biositemaps is the [http://bioportal.bioontology.org/visualize/40656 Biomedical Resource Ontology (BRO) V3] and [http://biositemaps.bioontology.org/editor/ Information Model (IM)] which is encapsulated in the Biositemaps Editor. [http://www.na-mic.org/Wiki/images/a/ac/Biositemaps_and_BRO_JBI-09-2691.pdf Here is the text of a paper on Biositemaps and BRO that was recently submitted with lead author Jessie Tennenbaum.] Also, please try out the new query tool: [http://www.biositemaps.org/rds Resource Discovery System (RDS)]. You can find the NCBC resources by selecting the "Resource Program" tab and then selecting 'NCBC'.<br />
*** ([http://www.loni.ucla.edu/~dinov Ivo Dinov]) [http://www.na-mic.org/Wiki/images/9/96/CCB_Supplement_Biositemaps_Pipeline_Report_2010.pdf Biositemaps.RDF Extension facilitating resource execution, invocation, input/output and process control, and interoperability].<br />
**** Example: CCB Biositemap.RDF<br />
***** [http://www.loni.ucla.edu/download/iTools/biositemap_NCBC_CCB.rdf Original (Standard RDF)]<br />
***** [http://www.na-mic.org/Wiki/images/e/e8/Biositemap_NCBC_CCB_PL_update021610.rdf Extended Biositemap_NCBC_CCB_PL_update021610.rdf]<br />
***** [http://www.na-mic.org/Wiki/images/1/16/Biositemap_NCBC_CCB_PL_update021610_ByRef.rdf Extended Biositemap_NCBC_CCB_PL_update021610_ByRef.rdf] (scalable by-reference version).<br />
**** Example Pipeline workflows ([http://www.na-mic.org/Wiki/images/3/3b/ND_WaveletTransform_WAIR.pipe.txt ND_WaveletTransform_WAIR.pipe], [http://www.na-mic.org/Wiki/images/1/12/ShapeTransform.pipe.txt ShapeTransform.pipe], [http://www.na-mic.org/Wiki/images/d/db/ShapeDistance.pipe.txt ShapeDistance.pipe]).<br />
**** [http://pipeline.loni.ucla.edu/support/xml-overview/ Pipeline XML Invocation Protocol].<br />
**** [http://www.loni.ucla.edu/twiki/bin/view/CCB/ITools_BiositemapsPipelineWorkflows See also this page].<br />
**** [http://www.loni.ucla.edu/twiki/bin/view/CCB/ITools_ReleaseNotes#iTools_V_1_12_Excel_XLS_Biositem iTools/Biositemaps XLS Support] (pending validation).<br />
*** Plans for adoption within and beyond NCBCs: CTSA, NIF, NITRC,IMAG,...<br />
** [[SDIWG:_NCBC_Scientific_Ontologies|Scientific Ontologies]]<br />
** [http://www.ncbcs.org/dbp_interactions.html NCBC Driving Biological Projects Interactions and Impact]<br />
**NCBC Dissemination and shared calendar: [http://wiki.simtk.org/ncbcdisseminate/ NCBC Dissemination page]. The [http://www.ncbcs.org/cal.html NCBC calendar] with [http://www.ncbcs.org/summary-cal.html NCBC RSS feeds for all centers]. Please check it out and provide feedback. (Joy)<br />
<br />
<br><br />
<br />
===Minutes===<br />
* '''Note taker''': [Suggested order of note takers for future meetings:'''Dinov (This one)''', Murphy (Next one), Ku, Schroeder, Floratos, Rubenson, Jags]<br />
* Review of [[SDIWG:Meeting_Minutes_20100219|February 19, 2010 Minutes]] <br />
* Attendees: David Rubenson, Ivo Dinov, Karen Skinner, Susanne Churchill, Gil Omenn, Trish Whetzel, Will Schroeder, Zohara Cohen, Peter Lyster, Jeannette Schmidt, Zak Kohane.<br />
<br />
* Peter/Zohara - [http://wiki.simtk.org/ncbcdisseminate/ dissemination efforts] / [http://www.ncbcs.org/cal.html NCBC Calendar]; [http://www.ncbcs.org/ NCBC web-page], [http://www.ncbcs.org/dbp_interactions.html DBP interactions] (access-stats, maps). How useful/used is the NCBC Calendar? Possible to add NCBC-Cal to Google/Personal Calendars. <br />
** Email and Calendars are now low-maintenance. <br />
** There are about 200 subscribers to this list (NCBC-Cal?)<br />
* Peter: Merger/Symbiosis of DBP and Calendar efforts.<br />
<br />
* Peter release of the [http://www.biositemaps.org/rds RDS (Resource Discovery System)].<br />
* CTSA/Biositemaps WG continues to make progress. Released RDS V.2?<br />
* Trish: latest efforts on [http://bioportal.bioontology.org/visualize/40656 BRO 3.1]. NCBC/CTSA collab - request from Pitt to include new regulatory branch - continually updated. Need to continue discussions on:<br />
** Update existing Biositemaps.RDF files and account for deprecated RDF constructs. Auto updates?<br />
** Extending the IM (Information model) to allow tool interoperability and comp-tool integration.<br />
** (Trish) Added announcements to BRO?<br />
** Send to Beth and Peter comments on RDS (2.0) functionality/operations/features.<br />
** Karen S: Any stats on RDS usage yet? Peter: Dev team is NCBC/Pitt - none of them are on this call (Peter will check with them).<br />
** BRO Paper (Jessie/Duke), in review.<br />
* Peter: RDF extension Pipelining: Ivo suggested drafting some details on hands-on utilization of the Biositemaps.RDF extension enabling the tool interoperability. <br />
* Peter: Action Items as above.<br />
* Peter: NCBC Renewal apps (June 15 review; Council Review Sept).<br />
** Susanne: Inter-interval/intermediate funding? <br />
** No-cost extension apps (at least until the end of August/September) - check with program officer.<br />
** Jeannette - assuming Aug/Sept (bridge?) difficult to plan.<br />
<br />
===Action Items===<br />
* TBD</div>Ivohttps://www.na-mic.org/w/index.php?title=SDIWG:Meeting_Minutes_20100528&diff=53111SDIWG:Meeting Minutes 201005282010-05-28T19:11:21Z<p>Ivo: /* Minutes */</p>
<hr />
<div>==NCBC Joint Working Group Meeting==<br />
<br />
[[SDIWG:Software_and_Data_Integration_Working_Group|Top page of SDIWG web site]]<br />
<br />
===Notes===<br />
''Friday May 28, 2010: 2:30-3:30 PM EST''<br><br />
''Please contact Peter Lyster for information [mailto:lysterp@mail.nih.gov Peter Lyster]''<br><br />
''[[SDIWG:Software_Engineering_Body_of_Knowledge_Across_NCBC_Biocomputing_Centers | SDIWG Meetings Page]]''<br><br />
<b>Save the date for the next SDWIG tcon/Connect, three months from now: August 20, 2010</b><br />
<br />
===Tcon DRAFT Agenda===<br />
<br />
*Roll Call/Note-taker (Ivo) (5 min)<br />
*Minutes from the last SDIWG tcon [[SDIWG:Meeting_Minutes_20100219|February 19, 2010]] (5 min)<br />
*Status check on '''working groups''': <br />
**[http://www.biositemaps.org Biositemaps] is a technology to address (i) describing, (ii) locating, (ii) querying, (iii) composing or combining, and (iv) navigating/mining biomedical resources. The underlying technology for Biositemaps is the [http://bioportal.bioontology.org/visualize/40656 Biomedical Resource Ontology (BRO) V3] and [http://biositemaps.bioontology.org/editor/ Information Model (IM)] which is encapsulated in the Biositemaps Editor. [http://www.na-mic.org/Wiki/images/a/ac/Biositemaps_and_BRO_JBI-09-2691.pdf Here is the text of a paper on Biositemaps and BRO that was recently submitted with lead author Jessie Tennenbaum.] Also, please try out the new query tool: [http://www.biositemaps.org/rds Resource Discovery System (RDS)]. You can find the NCBC resources by selecting the "Resource Program" tab and then selecting 'NCBC'.<br />
*** ([http://www.loni.ucla.edu/~dinov Ivo Dinov]) [http://www.na-mic.org/Wiki/images/9/96/CCB_Supplement_Biositemaps_Pipeline_Report_2010.pdf Biositemaps.RDF Extension facilitating resource execution, invocation, input/output and process control, and interoperability].<br />
**** Example: CCB Biositemap.RDF<br />
***** [http://www.loni.ucla.edu/download/iTools/biositemap_NCBC_CCB.rdf Original (Standard RDF)]<br />
***** [http://www.na-mic.org/Wiki/images/e/e8/Biositemap_NCBC_CCB_PL_update021610.rdf Extended Biositemap_NCBC_CCB_PL_update021610.rdf]<br />
***** [http://www.na-mic.org/Wiki/images/1/16/Biositemap_NCBC_CCB_PL_update021610_ByRef.rdf Extended Biositemap_NCBC_CCB_PL_update021610_ByRef.rdf] (scalable by-reference version).<br />
**** Example Pipeline workflows ([http://www.na-mic.org/Wiki/images/3/3b/ND_WaveletTransform_WAIR.pipe.txt ND_WaveletTransform_WAIR.pipe], [http://www.na-mic.org/Wiki/images/1/12/ShapeTransform.pipe.txt ShapeTransform.pipe], [http://www.na-mic.org/Wiki/images/d/db/ShapeDistance.pipe.txt ShapeDistance.pipe]).<br />
**** [http://pipeline.loni.ucla.edu/support/xml-overview/ Pipeline XML Invocation Protocol].<br />
**** [http://www.loni.ucla.edu/twiki/bin/view/CCB/ITools_BiositemapsPipelineWorkflows See also this page].<br />
**** [http://www.loni.ucla.edu/twiki/bin/view/CCB/ITools_ReleaseNotes#iTools_V_1_12_Excel_XLS_Biositem iTools/Biositemaps XLS Support] (pending validation).<br />
*** Plans for adoption within and beyond NCBCs: CTSA, NIF, NITRC,IMAG,...<br />
** [[SDIWG:_NCBC_Scientific_Ontologies|Scientific Ontologies]]<br />
** [http://www.ncbcs.org/dbp_interactions.html NCBC Driving Biological Projects Interactions and Impact]<br />
**NCBC Dissemination and shared calendar: [http://wiki.simtk.org/ncbcdisseminate/ NCBC Dissemination page]. The [http://www.ncbcs.org/cal.html NCBC calendar] with [http://www.ncbcs.org/summary-cal.html NCBC RSS feeds for all centers]. Please check it out and provide feedback. (Joy)<br />
<br />
<br><br />
<br />
===Minutes===<br />
* '''Note taker''': [Suggested order of note takers for future meetings:'''Dinov (This one)''', Murphy (Next one), Ku, Schroeder, Floratos, Rubenson, Jags]<br />
* Review of [[SDIWG:Meeting_Minutes_20100219|February 19, 2010 Minutes]] <br />
* Attendees: David Rubenson, Ivo Dinov, Karen Skinner, Susanne Churchill, Gil Omen, Trish Whetzel, Will Schroeder, Zohara Cohen, Peter Lyster, Jeannette Schmidt, Zak Kohane.<br />
<br />
* Peter/Zohara - [http://wiki.simtk.org/ncbcdisseminate/ dissemination efforts] / [http://www.ncbcs.org/cal.html NCBC Calendar]; [http://www.ncbcs.org/ NCBC web-page], [http://www.ncbcs.org/dbp_interactions.html DBP interactions] (access-stats, maps). How useful/used is the NCBC Calendar? Possible to add NCBC-Cal to Google/Personal Calendars. <br />
** Email and Calendars are now low-maintenance. <br />
** There are about 200 subscribers to this list (NCBC-Cal?)<br />
* Peter: Merger/Symbiosis of DBP and Calendar efforts.<br />
<br />
* Peter release of the [http://www.biositemaps.org/rds RDS (Resource Discovery System)].<br />
* CTSA/Biositemaps WG continues to make progress. Released RDS V.2?<br />
* Trish: latest efforts on [http://bioportal.bioontology.org/visualize/40656 BRO 3.1]. NCBC/CTSA collab - request from Pitt to include new regulatory branch - continually updated. Need to continue discussions on:<br />
** Update existing Biositemaps.RDF files and account for deprecated RDF constructs. Auto updates?<br />
** Extending the IM (Information model) to allow tool interoperability and comp-tool integration.<br />
** (Trish) Added announcements to BRO?<br />
** Send to Beth and Peter comments on RDS (2.0) functionality/operations/features.<br />
** Karen S: Any stats on RDS usage yet? Peter: Dev team is NCBC/Pitt - none of them are on this call (Peter will check with them).<br />
** BRO Paper (Jessie/Duke), in review.<br />
* Peter: RDF extension Pipelining: Ivo suggested drafting some details on hands-on utilization of the Biositemaps.RDF extension enabling the tool interoperability. <br />
* Peter: Action Items as above.<br />
* Peter: NCBC Renewal apps (June 15 review; Council Review Sept).<br />
** Susanne: Inter-interval/intermediate funding? <br />
** No-cost extension apps (at least until the end of August/September) - check with program officer.<br />
** Jeannette - assuming Aug/Sept (bridge?) difficult to plan.<br />
<br />
===Action Items===<br />
* TBD</div>Ivohttps://www.na-mic.org/w/index.php?title=SDIWG:Meeting_Minutes_20100528&diff=53110SDIWG:Meeting Minutes 201005282010-05-28T19:10:02Z<p>Ivo: /* Minutes */</p>
<hr />
<div>==NCBC Joint Working Group Meeting==<br />
<br />
[[SDIWG:Software_and_Data_Integration_Working_Group|Top page of SDIWG web site]]<br />
<br />
===Notes===<br />
''Friday May 28, 2010: 2:30-3:30 PM EST''<br><br />
''Please contact Peter Lyster for information [mailto:lysterp@mail.nih.gov Peter Lyster]''<br><br />
''[[SDIWG:Software_Engineering_Body_of_Knowledge_Across_NCBC_Biocomputing_Centers | SDIWG Meetings Page]]''<br><br />
<b>Save the date for the next SDWIG tcon/Connect, three months from now: August 20, 2010</b><br />
<br />
===Tcon DRAFT Agenda===<br />
<br />
*Roll Call/Note-taker (Ivo) (5 min)<br />
*Minutes from the last SDIWG tcon [[SDIWG:Meeting_Minutes_20100219|February 19, 2010]] (5 min)<br />
*Status check on '''working groups''': <br />
**[http://www.biositemaps.org Biositemaps] is a technology to address (i) describing, (ii) locating, (ii) querying, (iii) composing or combining, and (iv) navigating/mining biomedical resources. The underlying technology for Biositemaps is the [http://bioportal.bioontology.org/visualize/40656 Biomedical Resource Ontology (BRO) V3] and [http://biositemaps.bioontology.org/editor/ Information Model (IM)] which is encapsulated in the Biositemaps Editor. [http://www.na-mic.org/Wiki/images/a/ac/Biositemaps_and_BRO_JBI-09-2691.pdf Here is the text of a paper on Biositemaps and BRO that was recently submitted with lead author Jessie Tennenbaum.] Also, please try out the new query tool: [http://www.biositemaps.org/rds Resource Discovery System (RDS)]. You can find the NCBC resources by selecting the "Resource Program" tab and then selecting 'NCBC'.<br />
*** ([http://www.loni.ucla.edu/~dinov Ivo Dinov]) [http://www.na-mic.org/Wiki/images/9/96/CCB_Supplement_Biositemaps_Pipeline_Report_2010.pdf Biositemaps.RDF Extension facilitating resource execution, invocation, input/output and process control, and interoperability].<br />
**** Example: CCB Biositemap.RDF<br />
***** [http://www.loni.ucla.edu/download/iTools/biositemap_NCBC_CCB.rdf Original (Standard RDF)]<br />
***** [http://www.na-mic.org/Wiki/images/e/e8/Biositemap_NCBC_CCB_PL_update021610.rdf Extended Biositemap_NCBC_CCB_PL_update021610.rdf]<br />
***** [http://www.na-mic.org/Wiki/images/1/16/Biositemap_NCBC_CCB_PL_update021610_ByRef.rdf Extended Biositemap_NCBC_CCB_PL_update021610_ByRef.rdf] (scalable by-reference version).<br />
**** Example Pipeline workflows ([http://www.na-mic.org/Wiki/images/3/3b/ND_WaveletTransform_WAIR.pipe.txt ND_WaveletTransform_WAIR.pipe], [http://www.na-mic.org/Wiki/images/1/12/ShapeTransform.pipe.txt ShapeTransform.pipe], [http://www.na-mic.org/Wiki/images/d/db/ShapeDistance.pipe.txt ShapeDistance.pipe]).<br />
**** [http://pipeline.loni.ucla.edu/support/xml-overview/ Pipeline XML Invocation Protocol].<br />
**** [http://www.loni.ucla.edu/twiki/bin/view/CCB/ITools_BiositemapsPipelineWorkflows See also this page].<br />
**** [http://www.loni.ucla.edu/twiki/bin/view/CCB/ITools_ReleaseNotes#iTools_V_1_12_Excel_XLS_Biositem iTools/Biositemaps XLS Support] (pending validation).<br />
*** Plans for adoption within and beyond NCBCs: CTSA, NIF, NITRC,IMAG,...<br />
** [[SDIWG:_NCBC_Scientific_Ontologies|Scientific Ontologies]]<br />
** [http://www.ncbcs.org/dbp_interactions.html NCBC Driving Biological Projects Interactions and Impact]<br />
**NCBC Dissemination and shared calendar: [http://wiki.simtk.org/ncbcdisseminate/ NCBC Dissemination page]. The [http://www.ncbcs.org/cal.html NCBC calendar] with [http://www.ncbcs.org/summary-cal.html NCBC RSS feeds for all centers]. Please check it out and provide feedback. (Joy)<br />
<br />
<br><br />
<br />
===Minutes===<br />
* '''Note taker''': [Suggested order of note takers for future meetings:'''Dinov (This one)''', Murphy (Next one), Ku, Schroeder, Floratos, Rubenson, Jags]<br />
* Review of [[SDIWG:Meeting_Minutes_20100219|February 19, 2010 Minutes]] <br />
* Attendees: David Rubenson, Ivo Dinov, Karen Skinner, Susanne Churchill, Gil Omen, Trish Whetzel, Will Schroeder, Zohara Cohen, Peter Lyster, Jeannette Schmidt.<br />
<br />
* Peter/Zohara - [http://wiki.simtk.org/ncbcdisseminate/ dissemination efforts] / [http://www.ncbcs.org/cal.html NCBC Calendar]; [http://www.ncbcs.org/ NCBC web-page], [http://www.ncbcs.org/dbp_interactions.html DBP interactions] (access-stats, maps). How useful/used is the NCBC Calendar? Possible to add NCBC-Cal to Google/Personal Calendars. <br />
** Email and Calendars are now low-maintenance. <br />
** There are about 200 subscribers to this list (NCBC-Cal?)<br />
* Peter: Merger/Symbiosis of DBP and Calendar efforts.<br />
<br />
* Peter release of the [http://www.biositemaps.org/rds RDS (Resource Discovery System)].<br />
* CTSA/Biositemaps WG continues to make progress. Released RDS V.2?<br />
* Trish: latest efforts on [http://bioportal.bioontology.org/visualize/40656 BRO 3.1]. NCBC/CTSA collab - request from Pitt to include new regulatory branch - continually updated. Need to continue discussions on:<br />
** Update existing Biositemaps.RDF files and account for deprecated RDF constructs. Auto updates?<br />
** Extending the IM (Information model) to allow tool interoperability and comp-tool integration.<br />
** (Trish) Added announcements to BRO?<br />
** Send to Beth and Peter comments on RDS (2.0) functionality/operations/features.<br />
** Karen S: Any stats on RDS usage yet? Peter: Dev team is NCBC/Pitt - none of them are on this call (Peter will check with them).<br />
** BRO Paper (Jessie/Duke), in review.<br />
* Peter: RDF extension Pipelining: Ivo suggested drafting some details on hands-on utilization of the Biositemaps.RDF extension enabling the tool interoperability. <br />
* Peter: Action Items as above.<br />
* Peter: NCBC Renewal apps (June 15 review; Council Review Sept).<br />
** Susanne: Inter-interval/intermediate funding? <br />
** No-cost extension apps (at least until the end of August/September) - check with program officer.<br />
** Jeannette - assuming Aug/Sept (bridge?) difficult to plan.<br />
<br />
===Action Items===<br />
* TBD</div>Ivohttps://www.na-mic.org/w/index.php?title=SDIWG:Meeting_Minutes_20100528&diff=53109SDIWG:Meeting Minutes 201005282010-05-28T19:09:26Z<p>Ivo: /* Minutes */</p>
<hr />
<div>==NCBC Joint Working Group Meeting==<br />
<br />
[[SDIWG:Software_and_Data_Integration_Working_Group|Top page of SDIWG web site]]<br />
<br />
===Notes===<br />
''Friday May 28, 2010: 2:30-3:30 PM EST''<br><br />
''Please contact Peter Lyster for information [mailto:lysterp@mail.nih.gov Peter Lyster]''<br><br />
''[[SDIWG:Software_Engineering_Body_of_Knowledge_Across_NCBC_Biocomputing_Centers | SDIWG Meetings Page]]''<br><br />
<b>Save the date for the next SDWIG tcon/Connect, three months from now: August 20, 2010</b><br />
<br />
===Tcon DRAFT Agenda===<br />
<br />
*Roll Call/Note-taker (Ivo) (5 min)<br />
*Minutes from the last SDIWG tcon [[SDIWG:Meeting_Minutes_20100219|February 19, 2010]] (5 min)<br />
*Status check on '''working groups''': <br />
**[http://www.biositemaps.org Biositemaps] is a technology to address (i) describing, (ii) locating, (ii) querying, (iii) composing or combining, and (iv) navigating/mining biomedical resources. The underlying technology for Biositemaps is the [http://bioportal.bioontology.org/visualize/40656 Biomedical Resource Ontology (BRO) V3] and [http://biositemaps.bioontology.org/editor/ Information Model (IM)] which is encapsulated in the Biositemaps Editor. [http://www.na-mic.org/Wiki/images/a/ac/Biositemaps_and_BRO_JBI-09-2691.pdf Here is the text of a paper on Biositemaps and BRO that was recently submitted with lead author Jessie Tennenbaum.] Also, please try out the new query tool: [http://www.biositemaps.org/rds Resource Discovery System (RDS)]. You can find the NCBC resources by selecting the "Resource Program" tab and then selecting 'NCBC'.<br />
*** ([http://www.loni.ucla.edu/~dinov Ivo Dinov]) [http://www.na-mic.org/Wiki/images/9/96/CCB_Supplement_Biositemaps_Pipeline_Report_2010.pdf Biositemaps.RDF Extension facilitating resource execution, invocation, input/output and process control, and interoperability].<br />
**** Example: CCB Biositemap.RDF<br />
***** [http://www.loni.ucla.edu/download/iTools/biositemap_NCBC_CCB.rdf Original (Standard RDF)]<br />
***** [http://www.na-mic.org/Wiki/images/e/e8/Biositemap_NCBC_CCB_PL_update021610.rdf Extended Biositemap_NCBC_CCB_PL_update021610.rdf]<br />
***** [http://www.na-mic.org/Wiki/images/1/16/Biositemap_NCBC_CCB_PL_update021610_ByRef.rdf Extended Biositemap_NCBC_CCB_PL_update021610_ByRef.rdf] (scalable by-reference version).<br />
**** Example Pipeline workflows ([http://www.na-mic.org/Wiki/images/3/3b/ND_WaveletTransform_WAIR.pipe.txt ND_WaveletTransform_WAIR.pipe], [http://www.na-mic.org/Wiki/images/1/12/ShapeTransform.pipe.txt ShapeTransform.pipe], [http://www.na-mic.org/Wiki/images/d/db/ShapeDistance.pipe.txt ShapeDistance.pipe]).<br />
**** [http://pipeline.loni.ucla.edu/support/xml-overview/ Pipeline XML Invocation Protocol].<br />
**** [http://www.loni.ucla.edu/twiki/bin/view/CCB/ITools_BiositemapsPipelineWorkflows See also this page].<br />
**** [http://www.loni.ucla.edu/twiki/bin/view/CCB/ITools_ReleaseNotes#iTools_V_1_12_Excel_XLS_Biositem iTools/Biositemaps XLS Support] (pending validation).<br />
*** Plans for adoption within and beyond NCBCs: CTSA, NIF, NITRC,IMAG,...<br />
** [[SDIWG:_NCBC_Scientific_Ontologies|Scientific Ontologies]]<br />
** [http://www.ncbcs.org/dbp_interactions.html NCBC Driving Biological Projects Interactions and Impact]<br />
**NCBC Dissemination and shared calendar: [http://wiki.simtk.org/ncbcdisseminate/ NCBC Dissemination page]. The [http://www.ncbcs.org/cal.html NCBC calendar] with [http://www.ncbcs.org/summary-cal.html NCBC RSS feeds for all centers]. Please check it out and provide feedback. (Joy)<br />
<br />
<br><br />
<br />
===Minutes===<br />
* '''Note taker''': [Suggested order of note takers for future meetings:'''Dinov (This one)''', Murphy (Next one), Ku, Schroeder, Floratos, Rubenson, Jags]<br />
* Review of [[SDIWG:Meeting_Minutes_20100219|February 19, 2010 Minutes]] <br />
* Attendees: David Rubenson, Ivo Dinov, Karen Skinner, Susanne Churchill, Gil Omen, Trish Whetzel, Will Schroeder, Zohara Cohen, Peter Lister, Jeannette .<br />
<br />
* Peter/Zohara - [http://wiki.simtk.org/ncbcdisseminate/ dissemination efforts] / [http://www.ncbcs.org/cal.html NCBC Calendar]; [http://www.ncbcs.org/ NCBC web-page], [http://www.ncbcs.org/dbp_interactions.html DBP interactions] (access-stats, maps). How useful/used is the NCBC Calendar? Possible to add NCBC-Cal to Google/Personal Calendars. <br />
** Email and Calendars are now low-maintenance. <br />
** There are about 200 subscribers to this list (NCBC-Cal?)<br />
* Peter: Merger/Symbiosis of DBP and Calendar efforts.<br />
<br />
* Peter release of the [http://www.biositemaps.org/rds RDS (Resource Discovery System)].<br />
* CTSA/Biositemaps WG continues to make progress. Released RDS V.2?<br />
* Trish: latest efforts on [http://bioportal.bioontology.org/visualize/40656 BRO 3.1]. NCBC/CTSA collab - request from Pitt to include new regulatory branch - continually updated. Need to continue discussions on:<br />
** Update existing Biositemaps.RDF files and account for deprecated RDF constructs. Auto updates?<br />
** Extending the IM (Information model) to allow tool interoperability and comp-tool integration.<br />
** (Trish) Added announcements to BRO?<br />
** Send to Beth and Peter comments on RDS (2.0) functionality/operations/features.<br />
** Karen S: Any stats on RDS usage yet? Peter: Dev team is NCBC/Pitt - none of them are on this call (Peter will check with them).<br />
** BRO Paper (Jessie/Duke), in review.<br />
* Peter: RDF extension Pipelining: Ivo suggested drafting some details on hands-on utilization of the Biositemaps.RDF extension enabling the tool interoperability. <br />
* Peter: Action Items as above.<br />
* Peter: NCBC Renewal apps (June 15 review; Council Review Sept).<br />
** Susanne: Inter-interval/intermediate funding? <br />
** No-cost extension apps (at least until the end of August/September) - check with program officer.<br />
** Jeannette - assuming Aug/Sept (bridge?) difficult to plan.<br />
<br />
===Action Items===<br />
* TBD</div>Ivohttps://www.na-mic.org/w/index.php?title=SDIWG:Meeting_Minutes_20100528&diff=53107SDIWG:Meeting Minutes 201005282010-05-28T18:46:38Z<p>Ivo: /* Minutes */ added some notes</p>
<hr />
<div>==NCBC Joint Working Group Meeting==<br />
<br />
[[SDIWG:Software_and_Data_Integration_Working_Group|Top page of SDIWG web site]]<br />
<br />
===Notes===<br />
''Friday May 28, 2010: 2:30-3:30 PM EST''<br><br />
''Please contact Peter Lyster for information [mailto:lysterp@mail.nih.gov Peter Lyster]''<br><br />
''[[SDIWG:Software_Engineering_Body_of_Knowledge_Across_NCBC_Biocomputing_Centers | SDIWG Meetings Page]]''<br><br />
<b>Save the date for the next SDWIG tcon/Connect, three months from now: August 20, 2010</b><br />
<br />
===Tcon DRAFT Agenda===<br />
<br />
*Roll Call/Note-taker (Ivo) (5 min)<br />
*Minutes from the last SDIWG tcon [[SDIWG:Meeting_Minutes_20100219|February 19, 2010]] (5 min)<br />
*Status check on '''working groups''': <br />
**[http://www.biositemaps.org Biositemaps] is a technology to address (i) describing, (ii) locating, (ii) querying, (iii) composing or combining, and (iv) navigating/mining biomedical resources. The underlying technology for Biositemaps is the [http://bioportal.bioontology.org/visualize/40656 Biomedical Resource Ontology (BRO) V3] and [http://biositemaps.bioontology.org/editor/ Information Model (IM)] which is encapsulated in the Biositemaps Editor. [http://www.na-mic.org/Wiki/images/a/ac/Biositemaps_and_BRO_JBI-09-2691.pdf Here is the text of a paper on Biositemaps and BRO that was recently submitted with lead author Jessie Tennenbaum.] Also, please try out the new query tool: [http://www.biositemaps.org/rds Resource Discovery System (RDS)]. You can find the NCBC resources by selecting the "Resource Program" tab and then selecting 'NCBC'.<br />
*** ([http://www.loni.ucla.edu/~dinov Ivo Dinov]) [http://www.na-mic.org/Wiki/images/9/96/CCB_Supplement_Biositemaps_Pipeline_Report_2010.pdf Biositemaps.RDF Extension facilitating resource execution, invocation, input/output and process control, and interoperability].<br />
**** Example: CCB Biositemap.RDF<br />
***** [http://www.loni.ucla.edu/download/iTools/biositemap_NCBC_CCB.rdf Original (Standard RDF)]<br />
***** [http://www.na-mic.org/Wiki/images/e/e8/Biositemap_NCBC_CCB_PL_update021610.rdf Extended Biositemap_NCBC_CCB_PL_update021610.rdf]<br />
***** [http://www.na-mic.org/Wiki/images/1/16/Biositemap_NCBC_CCB_PL_update021610_ByRef.rdf Extended Biositemap_NCBC_CCB_PL_update021610_ByRef.rdf] (scalable by-reference version).<br />
**** Example Pipeline workflows ([http://www.na-mic.org/Wiki/images/3/3b/ND_WaveletTransform_WAIR.pipe.txt ND_WaveletTransform_WAIR.pipe], [http://www.na-mic.org/Wiki/images/1/12/ShapeTransform.pipe.txt ShapeTransform.pipe], [http://www.na-mic.org/Wiki/images/d/db/ShapeDistance.pipe.txt ShapeDistance.pipe]).<br />
**** [http://pipeline.loni.ucla.edu/support/xml-overview/ Pipeline XML Invocation Protocol].<br />
**** [http://www.loni.ucla.edu/twiki/bin/view/CCB/ITools_BiositemapsPipelineWorkflows See also this page].<br />
**** [http://www.loni.ucla.edu/twiki/bin/view/CCB/ITools_ReleaseNotes#iTools_V_1_12_Excel_XLS_Biositem iTools/Biositemaps XLS Support] (pending validation).<br />
*** Plans for adoption within and beyond NCBCs: CTSA, NIF, NITRC,IMAG,...<br />
** [[SDIWG:_NCBC_Scientific_Ontologies|Scientific Ontologies]]<br />
** [http://www.ncbcs.org/dbp_interactions.html NCBC Driving Biological Projects Interactions and Impact]<br />
**NCBC Dissemination and shared calendar: [http://wiki.simtk.org/ncbcdisseminate/ NCBC Dissemination page]. The [http://www.ncbcs.org/cal.html NCBC calendar] with [http://www.ncbcs.org/summary-cal.html NCBC RSS feeds for all centers]. Please check it out and provide feedback. (Joy)<br />
<br />
<br><br />
<br />
===Minutes===<br />
* '''Note taker''': [Suggested order of note takers for future meetings:'''Dinov (This one)''', Murphy (Next one), Ku, Schroeder, Floratos, Rubenson, Jags]<br />
* Review of [[SDIWG:Meeting_Minutes_20100219|February 19, 2010 Minutes]] <br />
* Attendees: David Rubenson, Ivo Dinov, Karen Skinner, Susanne Churchill, Gil Omen, Trish Whetzel, Will Schroeder, Zohara Cohen, Peter Lister.<br />
<br />
* Peter/Zohara - [http://wiki.simtk.org/ncbcdisseminate/ dissemination efforts] / [http://www.ncbcs.org/cal.html NCBC Calendar]; [http://www.ncbcs.org/ NCBC web-page], [http://www.ncbcs.org/dbp_interactions.html DBP interactions] (access-stats, maps). How useful/used is the NCBC Calendar? Possible to add NCBC-Cal to Google/Personal Calendars. <br />
** Email and Calendars are now low-maintenance. <br />
** There are about 200 subscribers to this list (NCBC-Cal?)<br />
* Peter: Merger/Symbiosis of DBP and Calendar efforts.<br />
<br />
* Peter release of the [http://www.biositemaps.org/rds RDS (Resource Discovery System)].<br />
* CTSA/Biositemaps WG continues to make progress. Released RDS V.2?<br />
* Trish: latest efforts on [ BRO]. NCBC/CTSA collab - request from Pitt to include new regulatory branch - continually updated. Need to continue discussions on:<br />
** Update existing Biositemaps.RDF files and account for deprecated RDF constructs. Auto updates?<br />
** Extending the IM (Information model) to allow tool interoperability and comp-tool integration.<br />
<br />
===Action Items===<br />
* TBD</div>Ivohttps://www.na-mic.org/w/index.php?title=SDIWG:Software_Engineering_Body_of_Knowledge_Across_NCBC_Biocomputing_Centers&diff=52961SDIWG:Software Engineering Body of Knowledge Across NCBC Biocomputing Centers2010-05-25T21:35:09Z<p>Ivo: /* Highlights from SDI TCONs */ replaced the list of meetings with a table</p>
<hr />
<div>== This Page contains the Regular Meeting Minutes and Discussions among the Seven NIH Roadmap National Centers for Biomedical Computing (NCBC) ==<br />
<br />
[[SDIWG:Software_and_Data_Integration_Working_Group|Top page of SDIWG web site]]<br />
<br />
----<br />
<br />
'''Charter of the Software and Data Integration (SDI) effort under the National Centers for Biomedical Computing (NCBC)'''<br />
<br />
The RFA states the goal of creating “the networked national effort to build the computational infrastructure for biomedical computing for the nation”. In furthering this, the goals of the SDIWG in concert with the Project Team and Centers staff are:<br />
<br />
1. To advance the domain sciences, and promote software interoperability and data exchange.<br />
<br />
2. To capture the collective knowledge of software engineering and practices among the Centers and publish this knowledge widely.<br />
<br />
More to follow...<br />
<br />
For questions about the activities of the SDIWG please contact the chair [mailto:lysterp@mail.nih.gov Peter Lyster]<br />
<br />
== Roadmap NCBC SDI Debrief Plans ==<br />
<br />
* [[SDIWG:Ongoing_Discussion|Summary of Initial Discussions on the Goals of the SDIWG including input from NCBCs]]<br />
<br />
== Highlights from SDI TCONs ==<br />
<br />
<center><br />
{| class="wikitable"<br />
|-<br />
! Year || Q1 || Q2 || Q3 || Q4<br />
|-<br />
| 2010 || [[SDIWG:Meeting_Minutes_20100219|SDIWG:Meeting Minutes 20100219]] || [[SDIWG:Meeting_Minutes_20100528|SDIWG:Meeting Minutes 20100528]] || 3 || 4 <br />
|-<br />
| 2009 || [[SDIWG:Meeting_Minutes_20090320|SDIWG:Meeting Minutes 20090320]] || 2 || 3 || [[SDIWG:Meeting_Minutes_20091120|SDIWG:Meeting Minutes 20091120]] <br />
|-<br />
| 2008 || [[SDIWG:Meeting_Minutes_20080222|SDIWG:Meeting Minutes 20080222]] || [[SDIWG:Meeting_Minutes_20080516|SDIWG:Meeting Minutes 20080516]] || [[SDIWG:Meeting_Minutes_20080919|SDIWG:Meeting Minutes 20080919]] || [[SDIWG:Meeting_Minutes_20081219|SDIWG:Meeting Minutes 20081219]] <br />
|-<br />
| 2007 || [[SDIWG:Meeting_Minutes_20070216|SDIWG:Meeting Minutes 20070216]] [[SDIWG:Meeting_Minutes_20070309|SDIWG:Meeting Minutes 20070309]] || [[SDIWG:Meeting_Minutes_20070518|SDIWG:Meeting Minutes 20070518]] ||[[SDIWG:Meeting_Minutes_20070921|SDIWG:Meeting Minutes 20070921]] || [[SDIWG:Meeting_Minutes_20071116|SDIWG:Meeting Minutes 20071116]] <br />
|-<br />
| 2006 || [[SDIWG:Meeting_Minutes_20060120|SDIWG:Meeting Minutes 20060120]] [[SDIWG:Meeting_Minutes_20060217|SDIWG:Meeting Minutes 20060217]] [[SDIWG:Meeting_Minutes_20060317|SDIWG:Meeting Minutes 20060317]] || [[SDIWG:Meeting_Minutes_20060421|SDIWG:Meeting Minutes 20060421]] [[SDIWG:Meeting_Minutes_20060519|SDIWG:Meeting Minutes 20060519]] [[SDIWG:Meeting_Minutes_20060616|SDIWG:Meeting Minutes 20060616]] || [[SDIWG:Meeting_Minutes_20060818|SDIWG:Meeting Minutes 20060818]] || [[SDIWG:Meeting_Minutes_20061117|SDIWG:Meeting Minutes 20061117]] <br />
|-<br />
| 2005 || [[SDIWG:Meeting_Minutes_20050218|SDIWG:Meeting Minutes 20050218]] [[SDIWG:Meeting_Minutes_20050318|SDIWG:Meeting Minutes 20050318]] || [[SDIWG:Meeting_Minutes_20050415|SDIWG:Meeting Minutes 20050415]] [[SDIWG:Meeting_Minutes_20050520|SDIWG:Meeting Minutes 20050520]] || [[SDIWG:Meeting_Minutes_20050617|SDIWG:Meeting Minutes 20050617]] [[SDIWG:Meeting_Minutes_20050819|SDIWG:Meeting Minutes 20050819]] || [[SDIWG:Meeting_Minutes_20050923|SDIWG:Meeting Minutes 20050923]] [[SDIWG:Meeting_Minutes_20051021|SDIWG:Meeting Minutes 20051021]] [[SDIWG:Meeting_Minutes_20051110|SDIWG:Meeting Minutes 20051110]] [[SDIWG:Meeting_Minutes_20051118|SDIWG:Meeting Minutes 20051118]]<br />
|}</div>Ivohttps://www.na-mic.org/w/index.php?title=SDIWG:Meeting_Minutes_20100528&diff=52852SDIWG:Meeting Minutes 201005282010-05-20T20:06:55Z<p>Ivo: /* Minutes */</p>
<hr />
<div>==NCBC Joint Working Group Meeting==<br />
<br />
[[SDIWG:Software_and_Data_Integration_Working_Group|Top page of SDIWG web site]]<br />
<br />
===Notes===<br />
''Friday May 28, 2010: 2:30-3:30 PM EST''<br><br />
''Please contact Peter Lyster for information [mailto:lysterp@mail.nih.gov Peter Lyster]''<br><br />
''[[SDIWG:Software_Engineering_Body_of_Knowledge_Across_NCBC_Biocomputing_Centers | SDIWG Meetings Page]]''<br><br />
<b>Save the date for the next SDWIG tcon/Connect, three months from now: August 20, 2010</b><br />
<br />
===Tcon DRAFT Agenda===<br />
<br />
*Roll Call/Note-taker (Ivo) (5 min)<br />
*Minutes from the last SDIWG tcon [[SDIWG:Meeting_Minutes_20100219|February 19, 2010]] (5 min)<br />
*Status check on '''working groups''': <br />
**[http://www.biositemaps.org Biositemaps] is a technology to address (i) describing, (ii) locating, (ii) querying, (iii) composing or combining, and (iv) navigating/mining biomedical resources. The underlying technology for Biositemaps is the [http://bioportal.bioontology.org/visualize/40656 Biomedical Resource Ontology (BRO) V3] and [http://biositemaps.bioontology.org/editor/ Information Model (IM)] which is encapsulated in the Biositemaps Editor. Please try it out the new query tool: [http://www.biositemaps.org/rds Resource Discovery System (RDS)]. You can find the NCBC resources by selecting the "Resource Program" tab and then selecting 'NCBC'.<br />
*** ([http://www.loni.ucla.edu/~dinov Ivo Dinov]) [http://www.na-mic.org/Wiki/images/9/96/CCB_Supplement_Biositemaps_Pipeline_Report_2010.pdf Biositemaps.RDF Extension facilitating resource execution, invocation, input/output and process control, and interoperability].<br />
**** Example: CCB Biositemap.RDF<br />
***** [http://www.loni.ucla.edu/download/iTools/biositemap_NCBC_CCB.rdf Original (Standard RDF)]<br />
***** [http://www.na-mic.org/Wiki/images/e/e8/Biositemap_NCBC_CCB_PL_update021610.rdf Extended Biositemap_NCBC_CCB_PL_update021610.rdf]<br />
***** [http://www.na-mic.org/Wiki/images/1/16/Biositemap_NCBC_CCB_PL_update021610_ByRef.rdf Extended Biositemap_NCBC_CCB_PL_update021610_ByRef.rdf] (scalable by-reference version).<br />
**** Example Pipeline workflows ([http://www.na-mic.org/Wiki/images/3/3b/ND_WaveletTransform_WAIR.pipe.txt ND_WaveletTransform_WAIR.pipe], [http://www.na-mic.org/Wiki/images/1/12/ShapeTransform.pipe.txt ShapeTransform.pipe], [http://www.na-mic.org/Wiki/images/d/db/ShapeDistance.pipe.txt ShapeDistance.pipe]).<br />
**** [http://pipeline.loni.ucla.edu/support/xml-overview/ Pipeline XML Invocation Protocol].<br />
**** [http://www.loni.ucla.edu/twiki/bin/view/CCB/ITools_BiositemapsPipelineWorkflows See also this page].<br />
**** [http://www.loni.ucla.edu/twiki/bin/view/CCB/ITools_ReleaseNotes#iTools_V_1_12_Excel_XLS_Biositem iTools/Biositemaps XLS Support] (pending validation).<br />
*** Plans for adoption within and beyond NCBCs: CTSA, NIF, NITRC,IMAG,...<br />
** [[SDIWG:_NCBC_Scientific_Ontologies|Scientific Ontologies]]<br />
** [http://www.ncbcs.org/dbp_interactions.html NCBC Driving Biological Projects Interactions and Impact]<br />
**NCBC Dissemination and shared calendar: [http://wiki.simtk.org/ncbcdisseminate/ NCBC Dissemination page]. The [http://www.ncbcs.org/cal.html NCBC calendar] with [http://www.ncbcs.org/summary-cal.html NCBC RSS feeds for all centers]. Please check it out and provide feedback. (Joy)<br />
<br />
<br><br />
<br />
===Minutes===<br />
* '''Note taker''': [Suggested order of note takers for future meetings:'''Dinov (This one)''', Murphy (Next one), Ku, Schroeder, Floratos, Rubenson, Jags]<br />
* Review of [[SDIWG:Meeting_Minutes_20100219|February 19, 2010 Minutes]] <br />
* Attendees:<br />
<br />
===Action Items===<br />
* TBD</div>Ivohttps://www.na-mic.org/w/index.php?title=SDIWG:Meeting_Minutes_20100528&diff=52851SDIWG:Meeting Minutes 201005282010-05-20T20:06:20Z<p>Ivo: /* Tcon DRAFT Agenda */</p>
<hr />
<div>==NCBC Joint Working Group Meeting==<br />
<br />
[[SDIWG:Software_and_Data_Integration_Working_Group|Top page of SDIWG web site]]<br />
<br />
===Notes===<br />
''Friday May 28, 2010: 2:30-3:30 PM EST''<br><br />
''Please contact Peter Lyster for information [mailto:lysterp@mail.nih.gov Peter Lyster]''<br><br />
''[[SDIWG:Software_Engineering_Body_of_Knowledge_Across_NCBC_Biocomputing_Centers | SDIWG Meetings Page]]''<br><br />
<b>Save the date for the next SDWIG tcon/Connect, three months from now: August 20, 2010</b><br />
<br />
===Tcon DRAFT Agenda===<br />
<br />
*Roll Call/Note-taker (Ivo) (5 min)<br />
*Minutes from the last SDIWG tcon [[SDIWG:Meeting_Minutes_20100219|February 19, 2010]] (5 min)<br />
*Status check on '''working groups''': <br />
**[http://www.biositemaps.org Biositemaps] is a technology to address (i) describing, (ii) locating, (ii) querying, (iii) composing or combining, and (iv) navigating/mining biomedical resources. The underlying technology for Biositemaps is the [http://bioportal.bioontology.org/visualize/40656 Biomedical Resource Ontology (BRO) V3] and [http://biositemaps.bioontology.org/editor/ Information Model (IM)] which is encapsulated in the Biositemaps Editor. Please try it out the new query tool: [http://www.biositemaps.org/rds Resource Discovery System (RDS)]. You can find the NCBC resources by selecting the "Resource Program" tab and then selecting 'NCBC'.<br />
*** ([http://www.loni.ucla.edu/~dinov Ivo Dinov]) [http://www.na-mic.org/Wiki/images/9/96/CCB_Supplement_Biositemaps_Pipeline_Report_2010.pdf Biositemaps.RDF Extension facilitating resource execution, invocation, input/output and process control, and interoperability].<br />
**** Example: CCB Biositemap.RDF<br />
***** [http://www.loni.ucla.edu/download/iTools/biositemap_NCBC_CCB.rdf Original (Standard RDF)]<br />
***** [http://www.na-mic.org/Wiki/images/e/e8/Biositemap_NCBC_CCB_PL_update021610.rdf Extended Biositemap_NCBC_CCB_PL_update021610.rdf]<br />
***** [http://www.na-mic.org/Wiki/images/1/16/Biositemap_NCBC_CCB_PL_update021610_ByRef.rdf Extended Biositemap_NCBC_CCB_PL_update021610_ByRef.rdf] (scalable by-reference version).<br />
**** Example Pipeline workflows ([http://www.na-mic.org/Wiki/images/3/3b/ND_WaveletTransform_WAIR.pipe.txt ND_WaveletTransform_WAIR.pipe], [http://www.na-mic.org/Wiki/images/1/12/ShapeTransform.pipe.txt ShapeTransform.pipe], [http://www.na-mic.org/Wiki/images/d/db/ShapeDistance.pipe.txt ShapeDistance.pipe]).<br />
**** [http://pipeline.loni.ucla.edu/support/xml-overview/ Pipeline XML Invocation Protocol].<br />
**** [http://www.loni.ucla.edu/twiki/bin/view/CCB/ITools_BiositemapsPipelineWorkflows See also this page].<br />
**** [http://www.loni.ucla.edu/twiki/bin/view/CCB/ITools_ReleaseNotes#iTools_V_1_12_Excel_XLS_Biositem iTools/Biositemaps XLS Support] (pending validation).<br />
*** Plans for adoption within and beyond NCBCs: CTSA, NIF, NITRC,IMAG,...<br />
** [[SDIWG:_NCBC_Scientific_Ontologies|Scientific Ontologies]]<br />
** [http://www.ncbcs.org/dbp_interactions.html NCBC Driving Biological Projects Interactions and Impact]<br />
**NCBC Dissemination and shared calendar: [http://wiki.simtk.org/ncbcdisseminate/ NCBC Dissemination page]. The [http://www.ncbcs.org/cal.html NCBC calendar] with [http://www.ncbcs.org/summary-cal.html NCBC RSS feeds for all centers]. Please check it out and provide feedback. (Joy)<br />
<br />
<br><br />
<br />
===Minutes===<br />
* '''Note taker''': [Suggested order of note takers for future meetings:'''Dinov (This one)''', Murphy (Next one), Ku, Schroeder, Floratos, Rubenson, Jags]<br />
* Review of [[SDIWG:Meeting_Minutes_20100219|February 19, 010 Minutes]] <br />
* Attendees:<br />
<br />
<br />
===Action Items===<br />
* TBD</div>Ivohttps://www.na-mic.org/w/index.php?title=SDIWG:Meeting_Minutes_20100528&diff=52850SDIWG:Meeting Minutes 201005282010-05-20T20:05:20Z<p>Ivo: </p>
<hr />
<div>==NCBC Joint Working Group Meeting==<br />
<br />
[[SDIWG:Software_and_Data_Integration_Working_Group|Top page of SDIWG web site]]<br />
<br />
===Notes===<br />
''Friday May 28, 2010: 2:30-3:30 PM EST''<br><br />
''Please contact Peter Lyster for information [mailto:lysterp@mail.nih.gov Peter Lyster]''<br><br />
''[[SDIWG:Software_Engineering_Body_of_Knowledge_Across_NCBC_Biocomputing_Centers | SDIWG Meetings Page]]''<br><br />
<b>Save the date for the next SDWIG tcon/Connect, three months from now: August 20, 2010</b><br />
<br />
===Tcon DRAFT Agenda===<br />
<br />
*Roll Call/Note-taker (Ivo) (5 min)<br />
*Minutes from the last SDIWG tcon [[SDIWG:Meeting_Minutes_20100219|February 19, 2010]] (5 min)<br />
*Status check on '''working groups''': <br />
**[http://www.biositemaps.org Biositemaps] is a technology to address (i) describing, (ii) locating, (ii) querying, (iii) composing or combining, and (iv) navigating/mining biomedical resources. The underlying technology for Biositemaps is the [http://bioportal.bioontology.org/visualize/40656 Biomedical Resource Ontology (BRO) V3] and [http://biositemaps.bioontology.org/editor/ Information Model (IM)] which is encapsulated in the Biositemaps Editor. Please try it out the new query tool: [http://www.biositemaps.org/rds Resource Discovery System (RDS)]. You can find the NCBC resources by selecting the "Resource Program" tab and then selecting 'NCBC'.<br />
*** ([http://www.loni.ucla.edu/~dinov Ivo Dinov]) [http://www.na-mic.org/Wiki/images/9/96/CCB_Supplement_Biositemaps_Pipeline_Report_2010.pdf Biositemaps.RDF Extension facilitating resource execution, invocation, input/output and process control, and interoperability].<br />
**** Example: CCB Biositemap.RDF<br />
***** [http://www.loni.ucla.edu/download/iTools/biositemap_NCBC_CCB.rdf Original (Standard RDF)]<br />
***** [http://www.na-mic.org/Wiki/images/e/e8/Biositemap_NCBC_CCB_PL_update021610.rdf Extended Biositemap_NCBC_CCB_PL_update021610.rdf]<br />
***** [http://www.na-mic.org/Wiki/images/1/16/Biositemap_NCBC_CCB_PL_update021610_ByRef.rdf Extended Biositemap_NCBC_CCB_PL_update021610_ByRef.rdf] (scalable by-reference version).<br />
**** Example Pipeline workflows ([http://www.na-mic.org/Wiki/images/3/3b/ND_WaveletTransform_WAIR.pipe.txt ND_WaveletTransform_WAIR.pipe], [http://www.na-mic.org/Wiki/images/1/12/ShapeTransform.pipe.txt ShapeTransform.pipe], [http://www.na-mic.org/Wiki/images/d/db/ShapeDistance.pipe.txt ShapeDistance.pipe]).<br />
**** [http://pipeline.loni.ucla.edu/support/xml-overview/ Pipeline XML Invocation Protocol].<br />
**** [http://www.loni.ucla.edu/twiki/bin/view/CCB/ITools_BiositemapsPipelineWorkflows See also this page].<br />
**** [http://www.loni.ucla.edu/twiki/bin/view/CCB/ITools_ReleaseNotes#iTools_V_1_12_Excel_XLS_Biositem iTools/Biositemaps XLS Support] (pending validation).<br />
*** Plans for adoption within and beyond NCBCs: CTSA, NIF, NITRC,IMAG,...<br />
** [[SDIWG:_NCBC_Scientific_Ontologies|Scientific Ontologies]]<br />
** [http://www.ncbcs.org/dbp_interactions.html NCBC Driving Biological Projects Interactions and Impact]<br />
**NCBC Dissemination and shared calendar: [http://wiki.simtk.org/ncbcdisseminate/ NCBC Dissemination page]. The [http://www.ncbcs.org/cal.html NCBC calendar] with RSS feeds available for each center at http://www.ncbcs.org/summary-cal.html. Please check it out and provide feedback. (Joy)<br />
<br />
<br><br />
<br />
===Minutes===<br />
* '''Note taker''': [Suggested order of note takers for future meetings:'''Dinov (This one)''', Murphy (Next one), Ku, Schroeder, Floratos, Rubenson, Jags]<br />
* Review of [[SDIWG:Meeting_Minutes_20100219|February 19, 010 Minutes]] <br />
* Attendees:<br />
<br />
<br />
===Action Items===<br />
* TBD</div>Ivohttps://www.na-mic.org/w/index.php?title=SDIWG:Meeting_Minutes_20100528&diff=52849SDIWG:Meeting Minutes 201005282010-05-20T20:03:20Z<p>Ivo: /* Tcon DRAFT Agenda */</p>
<hr />
<div>==NCBC Joint Working Group Meeting==<br />
<br />
[[SDIWG:Software_and_Data_Integration_Working_Group|Top page of SDIWG web site]]<br />
<br />
===Notes===<br />
''Friday May 28, 2010: 2:30-3:30 PM EST''<br><br />
''Please contact Peter Lyster for information [mailto:lysterp@mail.nih.gov Peter Lyster]''<br><br />
''[[SDIWG:Software_Engineering_Body_of_Knowledge_Across_NCBC_Biocomputing_Centers | SDIWG Meetings Page]]''<br><br />
<b>Save the date for the next SDWIG tcon/Connect, three months from now: August 20, 2010</b><br />
<br />
===Tcon DRAFT Agenda===<br />
<br />
*Roll Call/Note-taker (Ivo) (5 min)<br />
*Minutes from the last SDIWG tcon [[SDIWG:Meeting_Minutes_20100219|February 19, 2010]] (5 min)<br />
*Status check on '''working groups''': <br />
**[http://www.biositemaps.org Biositemaps] is a technology to address (i) describing, (ii) locating, (ii) querying, (iii) composing or combining, and (iv) navigating/mining biomedical resources. The underlying technology for Biositemaps is the [http://bioportal.bioontology.org/visualize/40656 Biomedical Resource Ontology (BRO) V3] and [http://biositemaps.bioontology.org/editor/ Information Model (IM)] which is encapsulated in the Biositemaps Editor. <b>Please try it out the new query tool: [http://www.biositemaps.org/rds Resource Discovery System (RDS)]</b> You can find the NCBC resources by selecting the "Resource Program" tab and then selecting 'NCBC'.<br />
*** ([http://www.loni.ucla.edu/~dinov Ivo Dinov]) [http://www.na-mic.org/Wiki/images/9/96/CCB_Supplement_Biositemaps_Pipeline_Report_2010.pdf Biositemaps.RDF Extension facilitating resource execution, invocation, input/output and process control, and interoperability].<br />
**** Example: CCB Biositemap.RDF<br />
***** [http://www.loni.ucla.edu/download/iTools/biositemap_NCBC_CCB.rdf Original (Standard RDF)]<br />
***** [http://www.na-mic.org/Wiki/images/e/e8/Biositemap_NCBC_CCB_PL_update021610.rdf Extended Biositemap_NCBC_CCB_PL_update021610.rdf]<br />
***** [http://www.na-mic.org/Wiki/images/1/16/Biositemap_NCBC_CCB_PL_update021610_ByRef.rdf Extended Biositemap_NCBC_CCB_PL_update021610_ByRef.rdf] (scalable by-reference version).<br />
**** Example Pipeline workflows ([http://www.na-mic.org/Wiki/images/3/3b/ND_WaveletTransform_WAIR.pipe.txt ND_WaveletTransform_WAIR.pipe], [http://www.na-mic.org/Wiki/images/1/12/ShapeTransform.pipe.txt ShapeTransform.pipe], [http://www.na-mic.org/Wiki/images/d/db/ShapeDistance.pipe.txt ShapeDistance.pipe]).<br />
**** [http://pipeline.loni.ucla.edu/support/xml-overview/ Pipeline XML Invocation Protocol].<br />
**** [http://www.loni.ucla.edu/twiki/bin/view/CCB/ITools_BiositemapsPipelineWorkflows See also this page].<br />
**** [http://www.loni.ucla.edu/twiki/bin/view/CCB/ITools_ReleaseNotes#iTools_V_1_12_Excel_XLS_Biositem iTools/Biositemaps XLS Support] (pending validation).<br />
*** Plans for adoption within and beyond NCBCs: CTSA, NIF, NITRC,IMAG,...<br />
** [[SDIWG:_NCBC_Scientific_Ontologies|Scientific Ontologies]]<br />
** [http://www.ncbcs.org/dbp_interactions.html NCBC Driving Biological Projects Interactions and Impact]<br />
**NCBC Dissemination and shared calendar: Dissemination page is at http://wiki.simtk.org/ncbcdisseminate/. The calendar is at http://www.ncbcs.org/cal.html with RSS feeds available for each center at http://www.ncbcs.org/summary-cal.html. Please check it out and provide feedback. (Joy)<br />
<br />
<br><br />
<br />
===Minutes===<br />
* '''Note taker''': [Suggested order of note takers for future meetings:'''Dinov (This one)''', Murphy (Next one), Ku, Schroeder, Floratos, Rubenson, Jags]<br />
* Review of [[SDIWG:Meeting_Minutes_20100219|February 19, 010 Minutes]] <br />
* Attendees:<br />
<br />
<br />
===Action Items===<br />
* TBD</div>Ivohttps://www.na-mic.org/w/index.php?title=SDIWG:Meeting_Minutes_20100219&diff=49071SDIWG:Meeting Minutes 201002192010-02-19T20:36:27Z<p>Ivo: /* Tcon DRAFT Agenda */</p>
<hr />
<div>==NCBC Joint Working Group Meeting==<br />
<br />
[[SDIWG:Software_and_Data_Integration_Working_Group|Top page of SDIWG web site]]<br />
<br />
===Notes===<br />
''Friday February 19, 2010: 2:30-3:30 PM EST''<br><br />
''Please contact Peter Lyster for information [mailto:lysterp@mail.nih.gov Peter Lyster]''<br><br />
''[[SDIWG:Software_Engineering_Body_of_Knowledge_Across_NCBC_Biocomputing_Centers | SDIWG Meetings Page]]''<br><br />
<b>Save the date for the next SDWIG tcon/Connect, three months from now: May 21, 2010</b><br />
<br />
===Tcon DRAFT Agenda===<br />
<br />
*Roll Call/Note-taker (Jags) (5 min)<br />
*Minutes from the last SDIWG tcon [[SDIWG:Meeting_Minutes_20091120|November 20, 2009]] (5 min)<br />
*Status check on '''working groups''': <br />
**[http://www.biositemaps.org Biositemaps] is a technology to address (i) locating, (ii) querying, (iii) composing or combining, and (iv) mining biomedical resources. The underlying technology for Biositemaps is the [http://bioportal.bioontology.org/visualize/40656 Biomedical Resource Ontology (BRO) V2.7.1] and the [http://biositemaps.bioontology.org/editor/ Information Model (IM) which is encapsulated in the Biositemaps Editor. Please try it out.]<br />
*** ([http://www.loni.ucla.edu/~dinov Ivo Dinov]) [http://www.na-mic.org/Wiki/images/9/96/CCB_Supplement_Biositemaps_Pipeline_Report_2010.pdf Biositemaps.RDF Extension facilitating resource execution, invocation, input/output and process control, and interoperability].<br />
**** Example: CCB Biositemap.RDF<br />
***** [http://www.loni.ucla.edu/download/iTools/biositemap_NCBC_CCB.rdf Original (Standard RDF)]<br />
***** [http://www.na-mic.org/Wiki/images/e/e8/Biositemap_NCBC_CCB_PL_update021610.rdf Extended Biositemap_NCBC_CCB_PL_update021610.rdf]<br />
***** [http://www.na-mic.org/Wiki/images/1/16/Biositemap_NCBC_CCB_PL_update021610_ByRef.rdf Extended Biositemap_NCBC_CCB_PL_update021610_ByRef.rdf] (scalable by-reference version).<br />
**** Example Pipeline workflows ([http://www.na-mic.org/Wiki/images/3/3b/ND_WaveletTransform_WAIR.pipe.txt ND_WaveletTransform_WAIR.pipe], [http://www.na-mic.org/Wiki/images/1/12/ShapeTransform.pipe.txt ShapeTransform.pipe], [http://www.na-mic.org/Wiki/images/d/db/ShapeDistance.pipe.txt ShapeDistance.pipe]).<br />
**** [http://pipeline.loni.ucla.edu/support/xml-overview/ Pipeline XML Invocation Protocol].<br />
**** [http://www.loni.ucla.edu/twiki/bin/view/CCB/ITools_BiositemapsPipelineWorkflows See also this page].<br />
**** [http://www.loni.ucla.edu/twiki/bin/view/CCB/ITools_ReleaseNotes#iTools_V_1_12_Excel_XLS_Biositem iTools/Biositemaps XLS Support] (pending validation).<br />
*** Plans for adoption within and beyond NCBCs: CTSA, NIF, NITRC,IMAG,...<br />
** [[SDIWG:_NCBC_Scientific_Ontologies|Scientific Ontologies]]<br />
** [http://www.ncbcs.org/map4.html NCBC Driving Biological Projects Interactions and Impact]<br />
**NCBC Dissemination and shared calendar: Dissemination page is at http://wiki.simtk.org/ncbcdisseminate/. The calendar is at http://www.ncbcs.org/cal.html with RSS feeds available for each center at http://www.ncbcs.org/summary-cal.html. Please check it out and provide feedback. (Joy)<br />
<br />
<br><br />
<br />
===Minutes===<br />
* '''Note taker''': [Suggested order of note takers for future meetings: '''Jags (this one)''', Dinov (next one), Murphy, Ku, Schroeder, Floratos, Rubenson]<br />
* Review of [[SDIWG:Meeting_Minutes_20091120|November 20, 2009 Minutes]] <br />
* Attendees: <br />
<br />
'''''Item 1'''''<br />
---------------------------------------<br />
*<br />
*<br />
*<br />
<br />
'''''Item 2'''''<br />
----------------------------------<br />
*<br />
*<br />
*<br />
<br />
'''''Item 3'''''<br />
-------------------<br />
*<br />
*<br />
*<br />
<br />
etc<br />
<br />
===Action Items===<br />
* TBD</div>Ivohttps://www.na-mic.org/w/index.php?title=SDIWG:Meeting_Minutes_20100219&diff=49070SDIWG:Meeting Minutes 201002192010-02-19T20:35:46Z<p>Ivo: /* Tcon DRAFT Agenda */</p>
<hr />
<div>==NCBC Joint Working Group Meeting==<br />
<br />
[[SDIWG:Software_and_Data_Integration_Working_Group|Top page of SDIWG web site]]<br />
<br />
===Notes===<br />
''Friday February 19, 2010: 2:30-3:30 PM EST''<br><br />
''Please contact Peter Lyster for information [mailto:lysterp@mail.nih.gov Peter Lyster]''<br><br />
''[[SDIWG:Software_Engineering_Body_of_Knowledge_Across_NCBC_Biocomputing_Centers | SDIWG Meetings Page]]''<br><br />
<b>Save the date for the next SDWIG tcon/Connect, three months from now: May 21, 2010</b><br />
<br />
===Tcon DRAFT Agenda===<br />
<br />
*Roll Call/Note-taker (Jags) (5 min)<br />
*Minutes from the last SDIWG tcon [[SDIWG:Meeting_Minutes_20091120|November 20, 2009]] (5 min)<br />
*Status check on '''working groups''': <br />
**[http://www.biositemaps.org Biositemaps] is a technology to address (i) locating, (ii) querying, (iii) composing or combining, and (iv) mining biomedical resources. The underlying technology for Biositemaps is the [http://bioportal.bioontology.org/visualize/40656 Biomedical Resource Ontology (BRO) V2.7.1] and the [http://biositemaps.bioontology.org/editor/ Information Model (IM) which is encapsulated in the Biositemaps Editor. Please try it out.]<br />
*** ([http://www.loni.ucla.edu/~dinov Ivo Dinov]) [http://www.na-mic.org/Wiki/images/9/96/CCB_Supplement_Biositemaps_Pipeline_Report_2010.pdf Biositemaps.RDF Extension facilitating resource execution, invocation, input/output and process control, and interoperability].<br />
**** Example: CCB Biositemap.RDF<br />
***** [http://www.loni.ucla.edu/download/iTools/biositemap_NCBC_CCB.rdf Original (Standard RDF)]<br />
***** [http://www.na-mic.org/Wiki/images/e/e8/Biositemap_NCBC_CCB_PL_update021610.rdf Extended Biositemap_NCBC_CCB_PL_update021610.rdf]<br />
***** [http://www.na-mic.org/Wiki/images/e/e8/Biositemap_NCBC_CCB_PL_update021610_ByRef.rdf Extended Biositemap_NCBC_CCB_PL_update021610_ByRef.rdf] (scalable by-reference version).<br />
**** Example Pipeline workflows ([http://www.na-mic.org/Wiki/images/3/3b/ND_WaveletTransform_WAIR.pipe.txt ND_WaveletTransform_WAIR.pipe], [http://www.na-mic.org/Wiki/images/1/12/ShapeTransform.pipe.txt ShapeTransform.pipe], [http://www.na-mic.org/Wiki/images/d/db/ShapeDistance.pipe.txt ShapeDistance.pipe]).<br />
**** [http://pipeline.loni.ucla.edu/support/xml-overview/ Pipeline XML Invocation Protocol].<br />
**** [http://www.loni.ucla.edu/twiki/bin/view/CCB/ITools_BiositemapsPipelineWorkflows See also this page].<br />
**** [http://www.loni.ucla.edu/twiki/bin/view/CCB/ITools_ReleaseNotes#iTools_V_1_12_Excel_XLS_Biositem iTools/Biositemaps XLS Support] (pending validation).<br />
*** Plans for adoption within and beyond NCBCs: CTSA, NIF, NITRC,IMAG,...<br />
** [[SDIWG:_NCBC_Scientific_Ontologies|Scientific Ontologies]]<br />
** [http://www.ncbcs.org/map4.html NCBC Driving Biological Projects Interactions and Impact]<br />
**NCBC Dissemination and shared calendar: Dissemination page is at http://wiki.simtk.org/ncbcdisseminate/. The calendar is at http://www.ncbcs.org/cal.html with RSS feeds available for each center at http://www.ncbcs.org/summary-cal.html. Please check it out and provide feedback. (Joy)<br />
<br />
<br><br />
<br />
===Minutes===<br />
* '''Note taker''': [Suggested order of note takers for future meetings: '''Jags (this one)''', Dinov (next one), Murphy, Ku, Schroeder, Floratos, Rubenson]<br />
* Review of [[SDIWG:Meeting_Minutes_20091120|November 20, 2009 Minutes]] <br />
* Attendees: <br />
<br />
'''''Item 1'''''<br />
---------------------------------------<br />
*<br />
*<br />
*<br />
<br />
'''''Item 2'''''<br />
----------------------------------<br />
*<br />
*<br />
*<br />
<br />
'''''Item 3'''''<br />
-------------------<br />
*<br />
*<br />
*<br />
<br />
etc<br />
<br />
===Action Items===<br />
* TBD</div>Ivohttps://www.na-mic.org/w/index.php?title=File:Biositemap_NCBC_CCB_PL_update021610.rdf&diff=49069File:Biositemap NCBC CCB PL update021610.rdf2010-02-19T20:34:46Z<p>Ivo: </p>
<hr />
<div></div>Ivohttps://www.na-mic.org/w/index.php?title=File:Biositemap_NCBC_CCB_PL_update021610_ByRef.rdf&diff=49068File:Biositemap NCBC CCB PL update021610 ByRef.rdf2010-02-19T20:34:08Z<p>Ivo: </p>
<hr />
<div></div>Ivohttps://www.na-mic.org/w/index.php?title=SDIWG:Meeting_Minutes_20100219&diff=49066SDIWG:Meeting Minutes 201002192010-02-19T19:28:56Z<p>Ivo: /* Tcon DRAFT Agenda */</p>
<hr />
<div>==NCBC Joint Working Group Meeting==<br />
<br />
[[SDIWG:Software_and_Data_Integration_Working_Group|Top page of SDIWG web site]]<br />
<br />
===Notes===<br />
''Friday February 19, 2010: 2:30-3:30 PM EST''<br><br />
''Please contact Peter Lyster for information [mailto:lysterp@mail.nih.gov Peter Lyster]''<br><br />
''[[SDIWG:Software_Engineering_Body_of_Knowledge_Across_NCBC_Biocomputing_Centers | SDIWG Meetings Page]]''<br><br />
<b>Save the date for the next SDWIG tcon/Connect, three months from now: May 21, 2010</b><br />
<br />
===Tcon DRAFT Agenda===<br />
<br />
*Roll Call/Note-taker (Jags) (5 min)<br />
*Minutes from the last SDIWG tcon [[SDIWG:Meeting_Minutes_20091120|November 20, 2009]] (5 min)<br />
*Status check on '''working groups''': <br />
**[http://www.biositemaps.org Biositemaps] is a technology to address (i) locating, (ii) querying, (iii) composing or combining, and (iv) mining biomedical resources. The underlying technology for Biositemaps is the [http://bioportal.bioontology.org/visualize/40656 Biomedical Resource Ontology (BRO) V2.7.1] and the [http://biositemaps.bioontology.org/editor/ Information Model (IM) which is encapsulated in the Biositemaps Editor. Please try it out.]<br />
*** ([http://www.loni.ucla.edu/~dinov Ivo Dinov]) [http://www.na-mic.org/Wiki/images/9/96/CCB_Supplement_Biositemaps_Pipeline_Report_2010.pdf Biositemaps.RDF Extension facilitating resource execution, invocation, input/output and process control, and interoperability].<br />
**** Example: CCB Biositemap.RDF<br />
***** [http://www.loni.ucla.edu/download/iTools/biositemap_NCBC_CCB.rdf Original (Standard RDF)]<br />
***** [http://www.na-mic.org/Wiki/images/5/58/Biositemap_NCBC_CCB_PL_update021610.rdf.txt Extended Biositemap_NCBC_CCB_PL_update021610.rdf]<br />
**** Example Pipeline workflows ([http://www.na-mic.org/Wiki/images/3/3b/ND_WaveletTransform_WAIR.pipe.txt ND_WaveletTransform_WAIR.pipe], [http://www.na-mic.org/Wiki/images/1/12/ShapeTransform.pipe.txt ShapeTransform.pipe], [http://www.na-mic.org/Wiki/images/d/db/ShapeDistance.pipe.txt ShapeDistance.pipe]).<br />
**** [http://pipeline.loni.ucla.edu/support/xml-overview/ Pipeline XML Invocation Protocol].<br />
**** [http://www.loni.ucla.edu/twiki/bin/view/CCB/ITools_BiositemapsPipelineWorkflows See also this page].<br />
**** [http://www.loni.ucla.edu/twiki/bin/view/CCB/ITools_ReleaseNotes#iTools_V_1_12_Excel_XLS_Biositem iTools/Biositemaps XLS Support] (pending validation).<br />
*** Plans for adoption within and beyond NCBCs: CTSA, NIF, NITRC,IMAG,...<br />
** [[SDIWG:_NCBC_Scientific_Ontologies|Scientific Ontologies]]<br />
** [http://www.ncbcs.org/map4.html NCBC Driving Biological Projects Interactions and Impact]<br />
**NCBC Dissemination and shared calendar: Dissemination page is at http://wiki.simtk.org/ncbcdisseminate/. The calendar is at http://www.ncbcs.org/cal.html with RSS feeds available for each center at http://www.ncbcs.org/summary-cal.html. Please check it out and provide feedback. (Joy)<br />
<br />
<br><br />
<br />
===Minutes===<br />
* '''Note taker''': [Suggested order of note takers for future meetings: '''Jags (this one)''', Dinov (next one), Murphy, Ku, Schroeder, Floratos, Rubenson]<br />
* Review of [[SDIWG:Meeting_Minutes_20091120|November 20, 2009 Minutes]] <br />
* Attendees: <br />
<br />
'''''Item 1'''''<br />
---------------------------------------<br />
*<br />
*<br />
*<br />
<br />
'''''Item 2'''''<br />
----------------------------------<br />
*<br />
*<br />
*<br />
<br />
'''''Item 3'''''<br />
-------------------<br />
*<br />
*<br />
*<br />
<br />
etc<br />
<br />
===Action Items===<br />
* TBD</div>Ivohttps://www.na-mic.org/w/index.php?title=Biositemaps&diff=49065Biositemaps2010-02-19T18:37:29Z<p>Ivo: </p>
<hr />
<div>''' This is the main page for the NIH Roadmap National Centers for Biomedical Computing (NCBC) Working Group titled: Biositemaps and the Biomedical Resource Ontology (BRO) '''<br />
<br />
[[SDIWG:Software_and_Data_Integration_Working_Group|Top page of NCBC Working Groups web site]]<br />
<br />
Contacts for this Working Group are [http://www.loni.ucla.edu/~dinov/Dinov_Email.gif Ivo Dinov], [mailto:whetzel@stanford.edu Trish Whetzel], and [mailto:lysterp@mail.nih.gov Peter Lyster]<br />
<br />
For more information about the NCBCs visit the [http://www.ncbcs.org/ Top page of ncbcs.org web site which is maintained by the NCBCs themselves]<br />
<br />
Legacy [[SDIWG:_NCBC_Resource_Yellow_Pages_and_Software_Ontologies]] Page<br />
<br />
----<br />
<br />
'''Biositemaps Project'''<br />
<br />
The Biositemaps Working Group of the [http://www.ncbcs.org/ NIH Roadmap National Centers of Biomedical Computing (NCBC) (www.ncbcs.org)] has developed a standard for communicating information on the Internet about biomedical resources (tools, data, software, material, and services). <b>The official public site of the Biositemaps Project is http://www.biositemaps.org/</b> In addition, the working group is using the biositemaps standard to address (i) locating, (ii) querying, (iii) composing or combining, and (iv) mining biomedical resources on the Internet. Each site which intends to contribute to the inventory instantiates a file on its Internet site ‘'biositemap.rdf' which conforms to a defined Information Model and uses concepts from the Biomedical Resource Ontology (BRO) describe the resources. Each biositemap.rdf file is simply a list of controlled metadata about resources that your organization uses or believes are important to biomedical research. <br />
<br />
* The key enabling technologies are the [http://www.ncbcs.org/biositemaps/formatDescription.html Information Model (IM)] which is the list of metadata fields about each resource (Resource_name, description, contact_person, resource_type,...) and <br />
* The [http://bioportal.bioontology.org/visualize/39977 Biomedical Resource Ontology (BRO) v2.7] which is a controlled terminology for the 'resource_type', 'area_of_research', and 'biomedical_activity' and which is used to improve the sensitivity and specificity of web searches. This is under development by a number of NIH-funded researchers who have a combined interest in classification of biomedical resources. The publication site for BRO is the BioPortal.<br />
<br />
----<br />
<br />
'''CIRWP Project'''<br />
<br />
* CIRWP GForge project page: https://bmir-gforge.stanford.edu/gf/project/cirwp_project/<br />
* CIRWP Confluence page (password-protected): https://www.umms.med.umich.edu/confluence/display/CIRWPQT/Home<br />
<br />
<br />
----<br />
<br />
'''Current List of Biositemaps [[Feature_Requests | Feature Requests]]'''<br />
<br />
'''Current List of [[Search_Engines | Biositemaps Search Engines]]'''<br />
<br />
'''Current List of [[FAQs | Biositemaps FAQs]]'''<br />
<br />
'''Current List of [[URLs | URLS that are used by Biositemaps Developers]]'''<br />
<br />
'''Current List of [[Developers_Meetings_and_Minutes | Developers Meetings and Minutes]]<br />
<br />
----<br />
<br />
'''[http://www.na-mic.org/Wiki/index.php/SDIWG:_NCBC_Resource_Yellow_Pages_and_Software_Ontologies Archive Biositemaps/Resourceome/Yellow Pages Development Pages]'''<br />
* [http://itools.ccb.ucla.edu/ iTools] (biositemaps producer and consumer)<br />
<br />
Site last updated: 20090607</div>Ivohttps://www.na-mic.org/w/index.php?title=File:CCB_Supplement_Biositemaps_Pipeline_Report_2010.pdf&diff=49010File:CCB Supplement Biositemaps Pipeline Report 2010.pdf2010-02-18T19:21:44Z<p>Ivo: uploaded a new version of "File:CCB Supplement Biositemaps Pipeline Report 2010.pdf"</p>
<hr />
<div></div>Ivohttps://www.na-mic.org/w/index.php?title=SDIWG:Meeting_Minutes_20100219&diff=48946SDIWG:Meeting Minutes 201002192010-02-18T00:50:52Z<p>Ivo: /* Tcon DRAFT Agenda */</p>
<hr />
<div>==NCBC Joint Working Group Meeting==<br />
<br />
[[SDIWG:Software_and_Data_Integration_Working_Group|Top page of SDIWG web site]]<br />
<br />
===Notes===<br />
''Friday February 19, 2010: 2:30-3:30 PM EST''<br><br />
''Please contact Peter Lyster for information [mailto:lysterp@mail.nih.gov Peter Lyster]''<br><br />
''[[SDIWG:Software_Engineering_Body_of_Knowledge_Across_NCBC_Biocomputing_Centers | SDIWG Meetings Page]]''<br><br />
<b>Save the date for the next SDWIG tcon/Connect, three months from now: May 21, 2010</b><br />
<br />
===Tcon DRAFT Agenda===<br />
<br />
*Roll Call/Note-taker (Jags) (5 min)<br />
*Minutes from the last SDIWG tcon [[SDIWG:Meeting_Minutes_20091120|November 20, 2009]] (5 min)<br />
*Status check on '''working groups''': <br />
**[http://www.biositemaps.org Biositemaps] is a technology to address (i) locating, (ii) querying, (iii) composing or combining, and (iv) mining biomedical resources. The underlying technology for Biositemaps is the [http://bioportal.bioontology.org/visualize/40656 Biomedical Resource Ontology (BRO) V2.7.1] and the [http://biositemaps.bioontology.org/editor/ Information Model (IM) which is encapsulated in the Biositemaps Editor. Please try it out.]<br />
*** ([http://www.loni.ucla.edu/~dinov Ivo Dinov]) [http://www.na-mic.org/Wiki/images/9/96/CCB_Supplement_Biositemaps_Pipeline_Report_2010.pdf Biositemaps.RDF Extension facilitating resource execution, invocation, input/output and process control, and interoperability].<br />
**** Example: CCB Biositemap.RDF<br />
***** [http://www.loni.ucla.edu/download/iTools/biositemap_NCBC_CCB.rdf Original (Standard RDF)]<br />
***** [http://www.na-mic.org/Wiki/images/5/58/Biositemap_NCBC_CCB_PL_update021610.rdf.txt Extended Biositemap_NCBC_CCB_PL_update021610.rdf]<br />
**** Example Pipeline workflows ([http://www.na-mic.org/Wiki/images/3/3b/ND_WaveletTransform_WAIR.pipe.txt ND_WaveletTransform_WAIR.pipe], [http://www.na-mic.org/Wiki/images/1/12/ShapeTransform.pipe.txt ShapeTransform.pipe], [http://www.na-mic.org/Wiki/images/d/db/ShapeDistance.pipe.txt ShapeDistance.pipe]).<br />
**** [http://pipeline.loni.ucla.edu/support/xml-overview/ Pipeline XML Invocation Protocol].<br />
**** [http://www.loni.ucla.edu/twiki/bin/view/CCB/ITools_BiositemapsPipelineWorkflows See also this page].<br />
*** Plans for adoption within and beyond NCBCs: CTSA, NIF, NITRC,IMAG,...<br />
** [[SDIWG:_NCBC_Scientific_Ontologies|Scientific Ontologies]]<br />
** [http://www.ncbcs.org/map4.html NCBC Driving Biological Projects Interactions and Impact]<br />
**NCBC Dissemination and shared calendar: Dissemination page is at http://wiki.simtk.org/ncbcdisseminate/. The calendar is at http://www.ncbcs.org/cal.html with RSS feeds available for each center at http://www.ncbcs.org/summary-cal.html. Please check it out and provide feedback. (Joy)<br />
<br />
<br><br />
<br />
===Minutes===<br />
* '''Note taker''': [Suggested order of note takers for future meetings: '''Jags (this one)''', Dinov (next one), Murphy, Ku, Schroeder, Floratos, Rubenson]<br />
* Review of [[SDIWG:Meeting_Minutes_20091120|November 20, 2009 Minutes]] <br />
* Attendees: <br />
<br />
'''''Item 1'''''<br />
---------------------------------------<br />
*<br />
*<br />
*<br />
<br />
'''''Item 2'''''<br />
----------------------------------<br />
*<br />
*<br />
*<br />
<br />
'''''Item 3'''''<br />
-------------------<br />
*<br />
*<br />
*<br />
<br />
etc<br />
<br />
===Action Items===<br />
* TBD</div>Ivohttps://www.na-mic.org/w/index.php?title=File:CCB_Supplement_Biositemaps_Pipeline_Report_2010.pdf&diff=48945File:CCB Supplement Biositemaps Pipeline Report 2010.pdf2010-02-18T00:33:04Z<p>Ivo: uploaded a new version of "File:CCB Supplement Biositemaps Pipeline Report 2010.pdf"</p>
<hr />
<div></div>Ivohttps://www.na-mic.org/w/index.php?title=File:Biositemap_NCBC_CCB_PL_update021610.rdf.txt&diff=48944File:Biositemap NCBC CCB PL update021610.rdf.txt2010-02-18T00:32:42Z<p>Ivo: uploaded a new version of "File:Biositemap NCBC CCB PL update021610.rdf.txt"</p>
<hr />
<div></div>Ivohttps://www.na-mic.org/w/index.php?title=File:Biositemap_NCBC_CCB_PL_update021610.rdf.txt&diff=48936File:Biositemap NCBC CCB PL update021610.rdf.txt2010-02-17T21:58:26Z<p>Ivo: uploaded a new version of "File:Biositemap NCBC CCB PL update021610.rdf.txt"</p>
<hr />
<div></div>Ivohttps://www.na-mic.org/w/index.php?title=File:CCB_Supplement_Biositemaps_Pipeline_Report_2010.pdf&diff=48935File:CCB Supplement Biositemaps Pipeline Report 2010.pdf2010-02-17T21:57:57Z<p>Ivo: uploaded a new version of "File:CCB Supplement Biositemaps Pipeline Report 2010.pdf"</p>
<hr />
<div></div>Ivohttps://www.na-mic.org/w/index.php?title=File:Biositemap_NCBC_CCB_PL_update021610.rdf.txt&diff=48934File:Biositemap NCBC CCB PL update021610.rdf.txt2010-02-17T21:47:47Z<p>Ivo: uploaded a new version of "File:Biositemap NCBC CCB PL update021610.rdf.txt"</p>
<hr />
<div></div>Ivohttps://www.na-mic.org/w/index.php?title=File:CCB_Supplement_Biositemaps_Pipeline_Report_2010.pdf&diff=48933File:CCB Supplement Biositemaps Pipeline Report 2010.pdf2010-02-17T21:47:16Z<p>Ivo: uploaded a new version of "File:CCB Supplement Biositemaps Pipeline Report 2010.pdf"</p>
<hr />
<div></div>Ivohttps://www.na-mic.org/w/index.php?title=SDIWG:Meeting_Minutes_20100219&diff=48792SDIWG:Meeting Minutes 201002192010-02-16T21:13:12Z<p>Ivo: /* Tcon DRAFT Agenda */</p>
<hr />
<div>==NCBC Joint Working Group Meeting==<br />
<br />
[[SDIWG:Software_and_Data_Integration_Working_Group|Top page of SDIWG web site]]<br />
<br />
===Notes===<br />
''Friday February 19, 2010: 2:30-3:30 PM EST''<br><br />
''Please contact Peter Lyster for information [mailto:lysterp@mail.nih.gov Peter Lyster]''<br><br />
''[[SDIWG:Software_Engineering_Body_of_Knowledge_Across_NCBC_Biocomputing_Centers | SDIWG Meetings Page]]''<br><br />
<b>Save the date for the next SDWIG tcon/Connect, three months from now: May 21, 2010</b><br />
<br />
===Tcon DRAFT Agenda===<br />
<br />
*Roll Call/Note-taker (Jags) (5 min)<br />
*Minutes from the last SDIWG tcon [[SDIWG:Meeting_Minutes_20091120|November 20, 2009]] (5 min)<br />
*Status check on '''working groups''': <br />
**[http://www.biositemaps.org Biositemaps] is a technology to address (i) locating, (ii) querying, (iii) composing or combining, and (iv) mining biomedical resources. The underlying technology for Biositemaps is the [http://bioportal.bioontology.org/visualize/40656 Biomedical Resource Ontology (BRO) V2.7.1] and the [http://biositemaps.bioontology.org/editor/ Information Model (IM) which is encapsulated in the Biositemaps Editor. Please try it out.]<br />
*** ([http://www.loni.ucla.edu/~dinov Ivo Dinov]) [http://www.na-mic.org/Wiki/images/9/96/CCB_Supplement_Biositemaps_Pipeline_Report_2010.pdf Biositemaps.RDF Extension facilitating resource execution, invocation, input/output and process control, and interoperability].<br />
**** Example: CCB Biositemap.RDF<br />
***** [http://www.loni.ucla.edu/download/iTools/biositemap_NCBC_CCB.rdf Original (Standard RDF)]<br />
***** [http://www.na-mic.org/Wiki/images/5/58/Biositemap_NCBC_CCB_PL_update021610.rdf.txt Extended Biositemap_NCBC_CCB_PL_update021610.rdf]<br />
**** Example Pipeline workflows ([http://www.na-mic.org/Wiki/images/3/3b/ND_WaveletTransform_WAIR.pipe.txt ND_WaveletTransform_WAIR.pipe], [http://www.na-mic.org/Wiki/images/1/12/ShapeTransform.pipe.txt ShapeTransform.pipe], [http://www.na-mic.org/Wiki/images/d/db/ShapeDistance.pipe.txt ShapeDistance.pipe]).<br />
**** [http://pipeline.loni.ucla.edu/support/xml-overview/ Pipeline XML Invocation Protocol].<br />
*** Plans for adoption within and beyond NCBCs: CTSA, NIF, NITRC,IMAG,...<br />
** [[SDIWG:_NCBC_Scientific_Ontologies|Scientific Ontologies]]<br />
** [http://www.ncbcs.org/map4.html NCBC Driving Biological Projects Interactions and Impact]<br />
**NCBC Dissemination and shared calendar: Dissemination page is at http://wiki.simtk.org/ncbcdisseminate/. The calendar is at http://www.ncbcs.org/cal.html with RSS feeds available for each center at http://www.ncbcs.org/summary-cal.html. Please check it out and provide feedback. (Joy)<br />
<br />
<br><br />
<br />
===Minutes===<br />
* '''Note taker''': [Suggested order of note takers for future meetings: '''Jags (this one)''', Dinov (next one), Murphy, Ku, Schroeder, Floratos, Rubenson]<br />
* Review of [[SDIWG:Meeting_Minutes_20091120|November 20, 2009 Minutes]] <br />
* Attendees: <br />
<br />
'''''Item 1'''''<br />
---------------------------------------<br />
*<br />
*<br />
*<br />
<br />
'''''Item 2'''''<br />
----------------------------------<br />
*<br />
*<br />
*<br />
<br />
'''''Item 3'''''<br />
-------------------<br />
*<br />
*<br />
*<br />
<br />
etc<br />
<br />
===Action Items===<br />
* TBD</div>Ivohttps://www.na-mic.org/w/index.php?title=SDIWG:Meeting_Minutes_20100219&diff=48791SDIWG:Meeting Minutes 201002192010-02-16T21:12:58Z<p>Ivo: /* Tcon DRAFT Agenda */</p>
<hr />
<div>==NCBC Joint Working Group Meeting==<br />
<br />
[[SDIWG:Software_and_Data_Integration_Working_Group|Top page of SDIWG web site]]<br />
<br />
===Notes===<br />
''Friday February 19, 2010: 2:30-3:30 PM EST''<br><br />
''Please contact Peter Lyster for information [mailto:lysterp@mail.nih.gov Peter Lyster]''<br><br />
''[[SDIWG:Software_Engineering_Body_of_Knowledge_Across_NCBC_Biocomputing_Centers | SDIWG Meetings Page]]''<br><br />
<b>Save the date for the next SDWIG tcon/Connect, three months from now: May 21, 2010</b><br />
<br />
===Tcon DRAFT Agenda===<br />
<br />
*Roll Call/Note-taker (Jags) (5 min)<br />
*Minutes from the last SDIWG tcon [[SDIWG:Meeting_Minutes_20091120|November 20, 2009]] (5 min)<br />
*Status check on '''working groups''': <br />
**[http://www.biositemaps.org Biositemaps] is a technology to address (i) locating, (ii) querying, (iii) composing or combining, and (iv) mining biomedical resources. The underlying technology for Biositemaps is the [http://bioportal.bioontology.org/visualize/40656 Biomedical Resource Ontology (BRO) V2.7.1] and the [http://biositemaps.bioontology.org/editor/ Information Model (IM) which is encapsulated in the Biositemaps Editor. Please try it out.]<br />
*** ([http://www.loni.ucla.edu/~dinov Ivo Dinov]) [http://www.na-mic.org/Wiki/images/9/96/CCB_Supplement_Biositemaps_Pipeline_Report_2010.pdf Biositemaps.RDF Extension facilitating resource execution, invocation, input/output and process control, and interoperability].<br />
**** CCB Biositemap.RDF<br />
***** [http://www.loni.ucla.edu/download/iTools/biositemap_NCBC_CCB.rdf Original (Standard RDF)]<br />
***** [http://www.na-mic.org/Wiki/images/5/58/Biositemap_NCBC_CCB_PL_update021610.rdf.txt Extended Biositemap_NCBC_CCB_PL_update021610.rdf]<br />
**** Example Pipeline workflows ([http://www.na-mic.org/Wiki/images/3/3b/ND_WaveletTransform_WAIR.pipe.txt ND_WaveletTransform_WAIR.pipe], [http://www.na-mic.org/Wiki/images/1/12/ShapeTransform.pipe.txt ShapeTransform.pipe], [http://www.na-mic.org/Wiki/images/d/db/ShapeDistance.pipe.txt ShapeDistance.pipe]).<br />
**** [http://pipeline.loni.ucla.edu/support/xml-overview/ Pipeline XML Invocation Protocol].<br />
*** Plans for adoption within and beyond NCBCs: CTSA, NIF, NITRC,IMAG,...<br />
** [[SDIWG:_NCBC_Scientific_Ontologies|Scientific Ontologies]]<br />
** [http://www.ncbcs.org/map4.html NCBC Driving Biological Projects Interactions and Impact]<br />
**NCBC Dissemination and shared calendar: Dissemination page is at http://wiki.simtk.org/ncbcdisseminate/. The calendar is at http://www.ncbcs.org/cal.html with RSS feeds available for each center at http://www.ncbcs.org/summary-cal.html. Please check it out and provide feedback. (Joy)<br />
<br />
<br><br />
<br />
===Minutes===<br />
* '''Note taker''': [Suggested order of note takers for future meetings: '''Jags (this one)''', Dinov (next one), Murphy, Ku, Schroeder, Floratos, Rubenson]<br />
* Review of [[SDIWG:Meeting_Minutes_20091120|November 20, 2009 Minutes]] <br />
* Attendees: <br />
<br />
'''''Item 1'''''<br />
---------------------------------------<br />
*<br />
*<br />
*<br />
<br />
'''''Item 2'''''<br />
----------------------------------<br />
*<br />
*<br />
*<br />
<br />
'''''Item 3'''''<br />
-------------------<br />
*<br />
*<br />
*<br />
<br />
etc<br />
<br />
===Action Items===<br />
* TBD</div>Ivohttps://www.na-mic.org/w/index.php?title=SDIWG:Meeting_Minutes_20100219&diff=48790SDIWG:Meeting Minutes 201002192010-02-16T21:12:45Z<p>Ivo: /* Tcon DRAFT Agenda */</p>
<hr />
<div>==NCBC Joint Working Group Meeting==<br />
<br />
[[SDIWG:Software_and_Data_Integration_Working_Group|Top page of SDIWG web site]]<br />
<br />
===Notes===<br />
''Friday February 19, 2010: 2:30-3:30 PM EST''<br><br />
''Please contact Peter Lyster for information [mailto:lysterp@mail.nih.gov Peter Lyster]''<br><br />
''[[SDIWG:Software_Engineering_Body_of_Knowledge_Across_NCBC_Biocomputing_Centers | SDIWG Meetings Page]]''<br><br />
<b>Save the date for the next SDWIG tcon/Connect, three months from now: May 21, 2010</b><br />
<br />
===Tcon DRAFT Agenda===<br />
<br />
*Roll Call/Note-taker (Jags) (5 min)<br />
*Minutes from the last SDIWG tcon [[SDIWG:Meeting_Minutes_20091120|November 20, 2009]] (5 min)<br />
*Status check on '''working groups''': <br />
**[http://www.biositemaps.org Biositemaps] is a technology to address (i) locating, (ii) querying, (iii) composing or combining, and (iv) mining biomedical resources. The underlying technology for Biositemaps is the [http://bioportal.bioontology.org/visualize/40656 Biomedical Resource Ontology (BRO) V2.7.1] and the [http://biositemaps.bioontology.org/editor/ Information Model (IM) which is encapsulated in the Biositemaps Editor. Please try it out.]<br />
*** ([http://www.loni.ucla.edu/~dinov Ivo Dinov]) [http://www.na-mic.org/Wiki/images/9/96/CCB_Supplement_Biositemaps_Pipeline_Report_2010.pdf Biositemaps.RDF Extension facilitating resource execution, invocation, input/output and process control, and interoperability].<br />
**** CCB Biositemap.RDF<br />
***** [www.loni.ucla.edu/download/iTools/biositemap_NCBC_CCB.rdf Original (Standard RDF)]<br />
***** [http://www.na-mic.org/Wiki/images/5/58/Biositemap_NCBC_CCB_PL_update021610.rdf.txt Extended Biositemap_NCBC_CCB_PL_update021610.rdf]<br />
**** Example Pipeline workflows ([http://www.na-mic.org/Wiki/images/3/3b/ND_WaveletTransform_WAIR.pipe.txt ND_WaveletTransform_WAIR.pipe], [http://www.na-mic.org/Wiki/images/1/12/ShapeTransform.pipe.txt ShapeTransform.pipe], [http://www.na-mic.org/Wiki/images/d/db/ShapeDistance.pipe.txt ShapeDistance.pipe]).<br />
**** [http://pipeline.loni.ucla.edu/support/xml-overview/ Pipeline XML Invocation Protocol].<br />
*** Plans for adoption within and beyond NCBCs: CTSA, NIF, NITRC,IMAG,...<br />
** [[SDIWG:_NCBC_Scientific_Ontologies|Scientific Ontologies]]<br />
** [http://www.ncbcs.org/map4.html NCBC Driving Biological Projects Interactions and Impact]<br />
**NCBC Dissemination and shared calendar: Dissemination page is at http://wiki.simtk.org/ncbcdisseminate/. The calendar is at http://www.ncbcs.org/cal.html with RSS feeds available for each center at http://www.ncbcs.org/summary-cal.html. Please check it out and provide feedback. (Joy)<br />
<br />
<br><br />
<br />
===Minutes===<br />
* '''Note taker''': [Suggested order of note takers for future meetings: '''Jags (this one)''', Dinov (next one), Murphy, Ku, Schroeder, Floratos, Rubenson]<br />
* Review of [[SDIWG:Meeting_Minutes_20091120|November 20, 2009 Minutes]] <br />
* Attendees: <br />
<br />
'''''Item 1'''''<br />
---------------------------------------<br />
*<br />
*<br />
*<br />
<br />
'''''Item 2'''''<br />
----------------------------------<br />
*<br />
*<br />
*<br />
<br />
'''''Item 3'''''<br />
-------------------<br />
*<br />
*<br />
*<br />
<br />
etc<br />
<br />
===Action Items===<br />
* TBD</div>Ivohttps://www.na-mic.org/w/index.php?title=SDIWG:Meeting_Minutes_20100219&diff=48783SDIWG:Meeting Minutes 201002192010-02-16T20:58:27Z<p>Ivo: /* Tcon DRAFT Agenda */</p>
<hr />
<div>==NCBC Joint Working Group Meeting==<br />
<br />
[[SDIWG:Software_and_Data_Integration_Working_Group|Top page of SDIWG web site]]<br />
<br />
===Notes===<br />
''Friday February 19, 2010: 2:30-3:30 PM EST''<br><br />
''Please contact Peter Lyster for information [mailto:lysterp@mail.nih.gov Peter Lyster]''<br><br />
''[[SDIWG:Software_Engineering_Body_of_Knowledge_Across_NCBC_Biocomputing_Centers | SDIWG Meetings Page]]''<br><br />
<b>Save the date for the next SDWIG tcon/Connect, three months from now: May 21, 2010</b><br />
<br />
===Tcon DRAFT Agenda===<br />
<br />
*Roll Call/Note-taker (Jags) (5 min)<br />
*Minutes from the last SDIWG tcon [[SDIWG:Meeting_Minutes_20091120|November 20, 2009]] (5 min)<br />
*Status check on '''working groups''': <br />
**[http://www.biositemaps.org Biositemaps] is a technology to address (i) locating, (ii) querying, (iii) composing or combining, and (iv) mining biomedical resources. The underlying technology for Biositemaps is the [http://bioportal.bioontology.org/visualize/40656 Biomedical Resource Ontology (BRO) V2.7.1] and the [http://biositemaps.bioontology.org/editor/ Information Model (IM) which is encapsulated in the Biositemaps Editor. Please try it out.]<br />
*** ([http://www.loni.ucla.edu/~dinov Ivo Dinov]) [http://www.na-mic.org/Wiki/images/9/96/CCB_Supplement_Biositemaps_Pipeline_Report_2010.pdf Biositemaps.RDF Extension facilitating resource execution, invocation, input/output and process control, and interoperability].<br />
**** [http://www.na-mic.org/Wiki/images/5/58/Biositemap_NCBC_CCB_PL_update021610.rdf.txt Extension Biositemap_NCBC_CCB_PL_update021610.rdf]<br />
**** Example Pipeline workflows ([http://www.na-mic.org/Wiki/images/3/3b/ND_WaveletTransform_WAIR.pipe.txt ND_WaveletTransform_WAIR.pipe], [http://www.na-mic.org/Wiki/images/1/12/ShapeTransform.pipe.txt ShapeTransform.pipe], [http://www.na-mic.org/Wiki/images/d/db/ShapeDistance.pipe.txt ShapeDistance.pipe]).<br />
**** [http://pipeline.loni.ucla.edu/support/xml-overview/ Pipeline XML Invocation Protocol].<br />
*** Plans for adoption within and beyond NCBCs: CTSA, NIF, NITRC,IMAG,...<br />
** [[SDIWG:_NCBC_Scientific_Ontologies|Scientific Ontologies]]<br />
** [http://www.ncbcs.org/map4.html NCBC Driving Biological Projects Interactions and Impact]<br />
**NCBC Dissemination and shared calendar: Dissemination page is at http://wiki.simtk.org/ncbcdisseminate/. The calendar is at http://www.ncbcs.org/cal.html with RSS feeds available for each center at http://www.ncbcs.org/summary-cal.html. Please check it out and provide feedback. (Joy)<br />
<br />
<br><br />
<br />
===Minutes===<br />
* '''Note taker''': [Suggested order of note takers for future meetings: '''Jags (this one)''', Dinov (next one), Murphy, Ku, Schroeder, Floratos, Rubenson]<br />
* Review of [[SDIWG:Meeting_Minutes_20091120|November 20, 2009 Minutes]] <br />
* Attendees: <br />
<br />
'''''Item 1'''''<br />
---------------------------------------<br />
*<br />
*<br />
*<br />
<br />
'''''Item 2'''''<br />
----------------------------------<br />
*<br />
*<br />
*<br />
<br />
'''''Item 3'''''<br />
-------------------<br />
*<br />
*<br />
*<br />
<br />
etc<br />
<br />
===Action Items===<br />
* TBD</div>Ivohttps://www.na-mic.org/w/index.php?title=SDIWG:Meeting_Minutes_20100219&diff=48782SDIWG:Meeting Minutes 201002192010-02-16T20:57:33Z<p>Ivo: /* Tcon DRAFT Agenda */</p>
<hr />
<div>==NCBC Joint Working Group Meeting==<br />
<br />
[[SDIWG:Software_and_Data_Integration_Working_Group|Top page of SDIWG web site]]<br />
<br />
===Notes===<br />
''Friday February 19, 2010: 2:30-3:30 PM EST''<br><br />
''Please contact Peter Lyster for information [mailto:lysterp@mail.nih.gov Peter Lyster]''<br><br />
''[[SDIWG:Software_Engineering_Body_of_Knowledge_Across_NCBC_Biocomputing_Centers | SDIWG Meetings Page]]''<br><br />
<b>Save the date for the next SDWIG tcon/Connect, three months from now: May 21, 2010</b><br />
<br />
===Tcon DRAFT Agenda===<br />
<br />
*Roll Call/Note-taker (Jags) (5 min)<br />
*Minutes from the last SDIWG tcon [[SDIWG:Meeting_Minutes_20091120|November 20, 2009]] (5 min)<br />
*Status check on '''working groups''': <br />
**[http://www.biositemaps.org Biositemaps] is a technology to address (i) locating, (ii) querying, (iii) composing or combining, and (iv) mining biomedical resources. The underlying technology for Biositemaps is the [http://bioportal.bioontology.org/visualize/40656 Biomedical Resource Ontology (BRO) V2.7.1] and the [http://biositemaps.bioontology.org/editor/ Information Model (IM) which is encapsulated in the Biositemaps Editor. Please try it out.]<br />
*** ([http://www.loni.ucla.edu/~dinov Ivo Dinov]) [http://www.na-mic.org/Wiki/images/9/96/CCB_Supplement_Biositemaps_Pipeline_Report_2010.pdf Biositemaps.RDF Extension facilitating resource execution, invocation, input/output and process control, and interoperability].<br />
**** [http://www.na-mic.org/Wiki/images/5/58/Biositemap_NCBC_CCB_PL_update021610.rdf.txt Extension Biositemap_NCBC_CCB_PL_update021610.rdf]<br />
**** Example Pipeline workflows ([http://www.na-mic.org/Wiki/images/3/3b/ND_WaveletTransform_WAIR.pipe.txt ND_WaveletTransform_WAIR.pipe], [http://www.na-mic.org/Wiki/images/1/12/ShapeTransform.pipe.txt ShapeTransform.pipe], [http://www.na-mic.org/Wiki/images/d/db/ShapeDistance.pipe.txt ShapeDistance.pipe]).<br />
*** Plans for adoption within and beyond NCBCs: CTSA, NIF, NITRC,IMAG,...<br />
** [[SDIWG:_NCBC_Scientific_Ontologies|Scientific Ontologies]]<br />
** [http://www.ncbcs.org/map4.html NCBC Driving Biological Projects Interactions and Impact]<br />
**NCBC Dissemination and shared calendar: Dissemination page is at http://wiki.simtk.org/ncbcdisseminate/. The calendar is at http://www.ncbcs.org/cal.html with RSS feeds available for each center at http://www.ncbcs.org/summary-cal.html. Please check it out and provide feedback. (Joy)<br />
<br />
<br><br />
<br />
===Minutes===<br />
* '''Note taker''': [Suggested order of note takers for future meetings: '''Jags (this one)''', Dinov (next one), Murphy, Ku, Schroeder, Floratos, Rubenson]<br />
* Review of [[SDIWG:Meeting_Minutes_20091120|November 20, 2009 Minutes]] <br />
* Attendees: <br />
<br />
'''''Item 1'''''<br />
---------------------------------------<br />
*<br />
*<br />
*<br />
<br />
'''''Item 2'''''<br />
----------------------------------<br />
*<br />
*<br />
*<br />
<br />
'''''Item 3'''''<br />
-------------------<br />
*<br />
*<br />
*<br />
<br />
etc<br />
<br />
===Action Items===<br />
* TBD</div>Ivohttps://www.na-mic.org/w/index.php?title=File:ShapeDistance.pipe.txt&diff=48781File:ShapeDistance.pipe.txt2010-02-16T20:57:08Z<p>Ivo: </p>
<hr />
<div></div>Ivohttps://www.na-mic.org/w/index.php?title=SDIWG:Meeting_Minutes_20100219&diff=48780SDIWG:Meeting Minutes 201002192010-02-16T20:56:54Z<p>Ivo: /* Tcon DRAFT Agenda */</p>
<hr />
<div>==NCBC Joint Working Group Meeting==<br />
<br />
[[SDIWG:Software_and_Data_Integration_Working_Group|Top page of SDIWG web site]]<br />
<br />
===Notes===<br />
''Friday February 19, 2010: 2:30-3:30 PM EST''<br><br />
''Please contact Peter Lyster for information [mailto:lysterp@mail.nih.gov Peter Lyster]''<br><br />
''[[SDIWG:Software_Engineering_Body_of_Knowledge_Across_NCBC_Biocomputing_Centers | SDIWG Meetings Page]]''<br><br />
<b>Save the date for the next SDWIG tcon/Connect, three months from now: May 21, 2010</b><br />
<br />
===Tcon DRAFT Agenda===<br />
<br />
*Roll Call/Note-taker (Jags) (5 min)<br />
*Minutes from the last SDIWG tcon [[SDIWG:Meeting_Minutes_20091120|November 20, 2009]] (5 min)<br />
*Status check on '''working groups''': <br />
**[http://www.biositemaps.org Biositemaps] is a technology to address (i) locating, (ii) querying, (iii) composing or combining, and (iv) mining biomedical resources. The underlying technology for Biositemaps is the [http://bioportal.bioontology.org/visualize/40656 Biomedical Resource Ontology (BRO) V2.7.1] and the [http://biositemaps.bioontology.org/editor/ Information Model (IM) which is encapsulated in the Biositemaps Editor. Please try it out.]<br />
*** ([http://www.loni.ucla.edu/~dinov Ivo Dinov]) [http://www.na-mic.org/Wiki/images/9/96/CCB_Supplement_Biositemaps_Pipeline_Report_2010.pdf Biositemaps.RDF Extension facilitating resource execution, invocation, input/output and process control, and interoperability].<br />
**** [http://www.na-mic.org/Wiki/images/5/58/Biositemap_NCBC_CCB_PL_update021610.rdf.txt Extension Biositemap_NCBC_CCB_PL_update021610.rdf]<br />
**** Example Pipeline workflows ([http://www.na-mic.org/Wiki/images/3/3b/ND_WaveletTransform_WAIR.pipe.txt ND_WaveletTransform_WAIR.pipe], [http://www.na-mic.org/Wiki/images/1/12/ShapeTransform.pipe.txt ShapeTransform.pip], )<br />
*** Plans for adoption within and beyond NCBCs: CTSA, NIF, NITRC,IMAG,...<br />
** [[SDIWG:_NCBC_Scientific_Ontologies|Scientific Ontologies]]<br />
** [http://www.ncbcs.org/map4.html NCBC Driving Biological Projects Interactions and Impact]<br />
**NCBC Dissemination and shared calendar: Dissemination page is at http://wiki.simtk.org/ncbcdisseminate/. The calendar is at http://www.ncbcs.org/cal.html with RSS feeds available for each center at http://www.ncbcs.org/summary-cal.html. Please check it out and provide feedback. (Joy)<br />
<br />
<br><br />
<br />
===Minutes===<br />
* '''Note taker''': [Suggested order of note takers for future meetings: '''Jags (this one)''', Dinov (next one), Murphy, Ku, Schroeder, Floratos, Rubenson]<br />
* Review of [[SDIWG:Meeting_Minutes_20091120|November 20, 2009 Minutes]] <br />
* Attendees: <br />
<br />
'''''Item 1'''''<br />
---------------------------------------<br />
*<br />
*<br />
*<br />
<br />
'''''Item 2'''''<br />
----------------------------------<br />
*<br />
*<br />
*<br />
<br />
'''''Item 3'''''<br />
-------------------<br />
*<br />
*<br />
*<br />
<br />
etc<br />
<br />
===Action Items===<br />
* TBD</div>Ivohttps://www.na-mic.org/w/index.php?title=File:ShapeTransform.pipe.txt&diff=48779File:ShapeTransform.pipe.txt2010-02-16T20:56:35Z<p>Ivo: </p>
<hr />
<div></div>Ivohttps://www.na-mic.org/w/index.php?title=SDIWG:Meeting_Minutes_20100219&diff=48778SDIWG:Meeting Minutes 201002192010-02-16T20:56:24Z<p>Ivo: /* Tcon DRAFT Agenda */</p>
<hr />
<div>==NCBC Joint Working Group Meeting==<br />
<br />
[[SDIWG:Software_and_Data_Integration_Working_Group|Top page of SDIWG web site]]<br />
<br />
===Notes===<br />
''Friday February 19, 2010: 2:30-3:30 PM EST''<br><br />
''Please contact Peter Lyster for information [mailto:lysterp@mail.nih.gov Peter Lyster]''<br><br />
''[[SDIWG:Software_Engineering_Body_of_Knowledge_Across_NCBC_Biocomputing_Centers | SDIWG Meetings Page]]''<br><br />
<b>Save the date for the next SDWIG tcon/Connect, three months from now: May 21, 2010</b><br />
<br />
===Tcon DRAFT Agenda===<br />
<br />
*Roll Call/Note-taker (Jags) (5 min)<br />
*Minutes from the last SDIWG tcon [[SDIWG:Meeting_Minutes_20091120|November 20, 2009]] (5 min)<br />
*Status check on '''working groups''': <br />
**[http://www.biositemaps.org Biositemaps] is a technology to address (i) locating, (ii) querying, (iii) composing or combining, and (iv) mining biomedical resources. The underlying technology for Biositemaps is the [http://bioportal.bioontology.org/visualize/40656 Biomedical Resource Ontology (BRO) V2.7.1] and the [http://biositemaps.bioontology.org/editor/ Information Model (IM) which is encapsulated in the Biositemaps Editor. Please try it out.]<br />
*** ([http://www.loni.ucla.edu/~dinov Ivo Dinov]) [http://www.na-mic.org/Wiki/images/9/96/CCB_Supplement_Biositemaps_Pipeline_Report_2010.pdf Biositemaps.RDF Extension facilitating resource execution, invocation, input/output and process control, and interoperability].<br />
**** [http://www.na-mic.org/Wiki/images/5/58/Biositemap_NCBC_CCB_PL_update021610.rdf.txt Extension Biositemap_NCBC_CCB_PL_update021610.rdf]<br />
**** Example Pipeline workflows ([http://www.na-mic.org/Wiki/images/3/3b/ND_WaveletTransform_WAIR.pipe.txt ND_WaveletTransform_WAIR.pipe], )<br />
*** Plans for adoption within and beyond NCBCs: CTSA, NIF, NITRC,IMAG,...<br />
** [[SDIWG:_NCBC_Scientific_Ontologies|Scientific Ontologies]]<br />
** [http://www.ncbcs.org/map4.html NCBC Driving Biological Projects Interactions and Impact]<br />
**NCBC Dissemination and shared calendar: Dissemination page is at http://wiki.simtk.org/ncbcdisseminate/. The calendar is at http://www.ncbcs.org/cal.html with RSS feeds available for each center at http://www.ncbcs.org/summary-cal.html. Please check it out and provide feedback. (Joy)<br />
<br />
<br><br />
<br />
===Minutes===<br />
* '''Note taker''': [Suggested order of note takers for future meetings: '''Jags (this one)''', Dinov (next one), Murphy, Ku, Schroeder, Floratos, Rubenson]<br />
* Review of [[SDIWG:Meeting_Minutes_20091120|November 20, 2009 Minutes]] <br />
* Attendees: <br />
<br />
'''''Item 1'''''<br />
---------------------------------------<br />
*<br />
*<br />
*<br />
<br />
'''''Item 2'''''<br />
----------------------------------<br />
*<br />
*<br />
*<br />
<br />
'''''Item 3'''''<br />
-------------------<br />
*<br />
*<br />
*<br />
<br />
etc<br />
<br />
===Action Items===<br />
* TBD</div>Ivohttps://www.na-mic.org/w/index.php?title=File:ND_WaveletTransform_WAIR.pipe.txt&diff=48777File:ND WaveletTransform WAIR.pipe.txt2010-02-16T20:55:55Z<p>Ivo: </p>
<hr />
<div></div>Ivohttps://www.na-mic.org/w/index.php?title=SDIWG:Meeting_Minutes_20100219&diff=48776SDIWG:Meeting Minutes 201002192010-02-16T20:55:41Z<p>Ivo: /* Tcon DRAFT Agenda */</p>
<hr />
<div>==NCBC Joint Working Group Meeting==<br />
<br />
[[SDIWG:Software_and_Data_Integration_Working_Group|Top page of SDIWG web site]]<br />
<br />
===Notes===<br />
''Friday February 19, 2010: 2:30-3:30 PM EST''<br><br />
''Please contact Peter Lyster for information [mailto:lysterp@mail.nih.gov Peter Lyster]''<br><br />
''[[SDIWG:Software_Engineering_Body_of_Knowledge_Across_NCBC_Biocomputing_Centers | SDIWG Meetings Page]]''<br><br />
<b>Save the date for the next SDWIG tcon/Connect, three months from now: May 21, 2010</b><br />
<br />
===Tcon DRAFT Agenda===<br />
<br />
*Roll Call/Note-taker (Jags) (5 min)<br />
*Minutes from the last SDIWG tcon [[SDIWG:Meeting_Minutes_20091120|November 20, 2009]] (5 min)<br />
*Status check on '''working groups''': <br />
**[http://www.biositemaps.org Biositemaps] is a technology to address (i) locating, (ii) querying, (iii) composing or combining, and (iv) mining biomedical resources. The underlying technology for Biositemaps is the [http://bioportal.bioontology.org/visualize/40656 Biomedical Resource Ontology (BRO) V2.7.1] and the [http://biositemaps.bioontology.org/editor/ Information Model (IM) which is encapsulated in the Biositemaps Editor. Please try it out.]<br />
*** ([http://www.loni.ucla.edu/~dinov Ivo Dinov]) [http://www.na-mic.org/Wiki/images/9/96/CCB_Supplement_Biositemaps_Pipeline_Report_2010.pdf Biositemaps.RDF Extension facilitating resource execution, invocation, input/output and process control, and interoperability].<br />
**** [http://www.na-mic.org/Wiki/images/5/58/Biositemap_NCBC_CCB_PL_update021610.rdf.txt Extension Biositemap_NCBC_CCB_PL_update021610.rdf]<br />
**** <br />
*** Plans for adoption within and beyond NCBCs: CTSA, NIF, NITRC,IMAG,...<br />
** [[SDIWG:_NCBC_Scientific_Ontologies|Scientific Ontologies]]<br />
** [http://www.ncbcs.org/map4.html NCBC Driving Biological Projects Interactions and Impact]<br />
**NCBC Dissemination and shared calendar: Dissemination page is at http://wiki.simtk.org/ncbcdisseminate/. The calendar is at http://www.ncbcs.org/cal.html with RSS feeds available for each center at http://www.ncbcs.org/summary-cal.html. Please check it out and provide feedback. (Joy)<br />
<br />
<br><br />
<br />
===Minutes===<br />
* '''Note taker''': [Suggested order of note takers for future meetings: '''Jags (this one)''', Dinov (next one), Murphy, Ku, Schroeder, Floratos, Rubenson]<br />
* Review of [[SDIWG:Meeting_Minutes_20091120|November 20, 2009 Minutes]] <br />
* Attendees: <br />
<br />
'''''Item 1'''''<br />
---------------------------------------<br />
*<br />
*<br />
*<br />
<br />
'''''Item 2'''''<br />
----------------------------------<br />
*<br />
*<br />
*<br />
<br />
'''''Item 3'''''<br />
-------------------<br />
*<br />
*<br />
*<br />
<br />
etc<br />
<br />
===Action Items===<br />
* TBD</div>Ivohttps://www.na-mic.org/w/index.php?title=File:Biositemap_NCBC_CCB_PL_update021610.rdf.txt&diff=48774File:Biositemap NCBC CCB PL update021610.rdf.txt2010-02-16T20:54:28Z<p>Ivo: </p>
<hr />
<div></div>Ivohttps://www.na-mic.org/w/index.php?title=SDIWG:Meeting_Minutes_20100219&diff=48771SDIWG:Meeting Minutes 201002192010-02-16T20:48:47Z<p>Ivo: </p>
<hr />
<div>==NCBC Joint Working Group Meeting==<br />
<br />
[[SDIWG:Software_and_Data_Integration_Working_Group|Top page of SDIWG web site]]<br />
<br />
===Notes===<br />
''Friday February 19, 2010: 2:30-3:30 PM EST''<br><br />
''Please contact Peter Lyster for information [mailto:lysterp@mail.nih.gov Peter Lyster]''<br><br />
''[[SDIWG:Software_Engineering_Body_of_Knowledge_Across_NCBC_Biocomputing_Centers | SDIWG Meetings Page]]''<br><br />
<b>Save the date for the next SDWIG tcon/Connect, three months from now: May 21, 2010</b><br />
<br />
===Tcon DRAFT Agenda===<br />
<br />
*Roll Call/Note-taker (Jags) (5 min)<br />
*Minutes from the last SDIWG tcon [[SDIWG:Meeting_Minutes_20091120|November 20, 2009]] (5 min)<br />
*Status check on '''working groups''': <br />
**[http://www.biositemaps.org Biositemaps] is a technology to address (i) locating, (ii) querying, (iii) composing or combining, and (iv) mining biomedical resources. The underlying technology for Biositemaps is the [http://bioportal.bioontology.org/visualize/40656 Biomedical Resource Ontology (BRO) V2.7.1] and the [http://biositemaps.bioontology.org/editor/ Information Model (IM) which is encapsulated in the Biositemaps Editor. Please try it out.]<br />
*** ([http://www.loni.ucla.edu/~dinov Ivo Dinov]) [http://www.na-mic.org/Wiki/images/9/96/CCB_Supplement_Biositemaps_Pipeline_Report_2010.pdf Biositemaps.RDF Extension facilitating resource execution, invocation, input/output and process control, and interoperability].<br />
*** Plans for adoption within and beyond NCBCs: CTSA, NIF, NITRC,IMAG,...<br />
** [[SDIWG:_NCBC_Scientific_Ontologies|Scientific Ontologies]]<br />
** [http://www.ncbcs.org/map4.html NCBC Driving Biological Projects Interactions and Impact]<br />
**NCBC Dissemination and shared calendar: Dissemination page is at http://wiki.simtk.org/ncbcdisseminate/. The calendar is at http://www.ncbcs.org/cal.html with RSS feeds available for each center at http://www.ncbcs.org/summary-cal.html. Please check it out and provide feedback. (Joy)<br />
<br />
<br><br />
<br />
===Minutes===<br />
* '''Note taker''': [Suggested order of note takers for future meetings: '''Jags (this one)''', Dinov (next one), Murphy, Ku, Schroeder, Floratos, Rubenson]<br />
* Review of [[SDIWG:Meeting_Minutes_20091120|November 20, 2009 Minutes]] <br />
* Attendees: <br />
<br />
'''''Item 1'''''<br />
---------------------------------------<br />
*<br />
*<br />
*<br />
<br />
'''''Item 2'''''<br />
----------------------------------<br />
*<br />
*<br />
*<br />
<br />
'''''Item 3'''''<br />
-------------------<br />
*<br />
*<br />
*<br />
<br />
etc<br />
<br />
===Action Items===<br />
* TBD</div>Ivohttps://www.na-mic.org/w/index.php?title=File:CCB_Supplement_Biositemaps_Pipeline_Report_2010.pdf&diff=48768File:CCB Supplement Biositemaps Pipeline Report 2010.pdf2010-02-16T20:48:14Z<p>Ivo: </p>
<hr />
<div></div>Ivohttps://www.na-mic.org/w/index.php?title=SDIWG:Meeting_Minutes_20100219&diff=48767SDIWG:Meeting Minutes 201002192010-02-16T20:47:55Z<p>Ivo: /* Tcon DRAFT Agenda */</p>
<hr />
<div>==NCBC Joint Working Group Meeting==<br />
<br />
[[SDIWG:Software_and_Data_Integration_Working_Group|Top page of SDIWG web site]]<br />
<br />
===Notes===<br />
''Friday February 19, 2010: 2:30-3:30 PM EST''<br><br />
''Please contact Peter Lyster for information [mailto:lysterp@mail.nih.gov Peter Lyster]''<br><br />
''[[SDIWG:Software_Engineering_Body_of_Knowledge_Across_NCBC_Biocomputing_Centers | SDIWG Meetings Page]]''<br><br />
<b>Save the date for the next SDWIG tcon/Connect, three months from now: May 21, 2010</b><br />
<br />
===Tcon DRAFT Agenda===<br />
<br />
*Roll Call/Note-taker (Jags) (5 min)<br />
*Minutes from the last SDIWG tcon [[SDIWG:Meeting_Minutes_20091120|November 20, 2009]] (5 min)<br />
*Status check on '''working groups''': <br />
**[http://www.biositemaps.org Biositemaps] is a technology to address (i) locating, (ii) querying, (iii) composing or combining, and (iv) mining biomedical resources. The underlying technology for Biositemaps is the [http://bioportal.bioontology.org/visualize/40656 Biomedical Resource Ontology (BRO) V2.7.1] and the [http://biositemaps.bioontology.org/editor/ Information Model (IM) which is encapsulated in the Biositemaps Editor. Please try it out.]<br />
*** ([http://www.loni.ucla.edu/~dinov Ivo Dinov]) Biositemaps.RDF Extension facilitating resource execution, invocation, input/output and process control, and interoperability.<br />
*** Plans for adoption within and beyond NCBCs: CTSA, NIF, NITRC,IMAG,...<br />
** [[SDIWG:_NCBC_Scientific_Ontologies|Scientific Ontologies]]<br />
** [http://www.ncbcs.org/map4.html NCBC Driving Biological Projects Interactions and Impact]<br />
**NCBC Dissemination and shared calendar: Dissemination page is at http://wiki.simtk.org/ncbcdisseminate/. The calendar is at http://www.ncbcs.org/cal.html with RSS feeds available for each center at http://www.ncbcs.org/summary-cal.html. Please check it out and provide feedback. (Joy)<br />
<br />
<br><br />
<br />
===Minutes===<br />
* '''Note taker''': [Suggested order of note takers for future meetings: '''Jags (this one)''', Dinov (next one), Murphy, Ku, Schroeder, Floratos, Rubenson]<br />
* Review of [[SDIWG:Meeting_Minutes_20091120|November 20, 2009 Minutes]] <br />
* Attendees: <br />
<br />
'''''Item 1'''''<br />
---------------------------------------<br />
*<br />
*<br />
*<br />
<br />
'''''Item 2'''''<br />
----------------------------------<br />
*<br />
*<br />
*<br />
<br />
'''''Item 3'''''<br />
-------------------<br />
*<br />
*<br />
*<br />
<br />
etc<br />
<br />
===Action Items===<br />
* TBD</div>Ivohttps://www.na-mic.org/w/index.php?title=SDIWG:Meeting_Minutes_20100219&diff=48765SDIWG:Meeting Minutes 201002192010-02-16T20:47:35Z<p>Ivo: /* Tcon DRAFT Agenda */</p>
<hr />
<div>==NCBC Joint Working Group Meeting==<br />
<br />
[[SDIWG:Software_and_Data_Integration_Working_Group|Top page of SDIWG web site]]<br />
<br />
===Notes===<br />
''Friday February 19, 2010: 2:30-3:30 PM EST''<br><br />
''Please contact Peter Lyster for information [mailto:lysterp@mail.nih.gov Peter Lyster]''<br><br />
''[[SDIWG:Software_Engineering_Body_of_Knowledge_Across_NCBC_Biocomputing_Centers | SDIWG Meetings Page]]''<br><br />
<b>Save the date for the next SDWIG tcon/Connect, three months from now: May 21, 2010</b><br />
<br />
===Tcon DRAFT Agenda===<br />
<br />
*Roll Call/Note-taker (Jags) (5 min)<br />
*Minutes from the last SDIWG tcon [[SDIWG:Meeting_Minutes_20091120|November 20, 2009]] (5 min)<br />
*Status check on '''working groups''': <br />
**[http://www.biositemaps.org Biositemaps] is a technology to address (i) locating, (ii) querying, (iii) composing or combining, and (iv) mining biomedical resources. The underlying technology for Biositemaps is the [http://bioportal.bioontology.org/visualize/40656 Biomedical Resource Ontology (BRO) V2.7.1] and the [http://biositemaps.bioontology.org/editor/ Information Model (IM) which is encapsulated in the Biositemaps Editor. Please try it out.]<br />
([http://www.loni.ucla.edu/~dinov Ivo Dinov]) Biositemaps.RDF Extension facilitating resource execution, invocation, input/output and process control, and interoperability.*** Plans for adoption within and beyond NCBCs: CTSA, NIF, NITRC,IMAG,...<br />
** [[SDIWG:_NCBC_Scientific_Ontologies|Scientific Ontologies]]<br />
** [http://www.ncbcs.org/map4.html NCBC Driving Biological Projects Interactions and Impact]<br />
**NCBC Dissemination and shared calendar: Dissemination page is at http://wiki.simtk.org/ncbcdisseminate/. The calendar is at http://www.ncbcs.org/cal.html with RSS feeds available for each center at http://www.ncbcs.org/summary-cal.html. Please check it out and provide feedback. (Joy)<br />
<br />
<br><br />
<br />
===Minutes===<br />
* '''Note taker''': [Suggested order of note takers for future meetings: '''Jags (this one)''', Dinov (next one), Murphy, Ku, Schroeder, Floratos, Rubenson]<br />
* Review of [[SDIWG:Meeting_Minutes_20091120|November 20, 2009 Minutes]] <br />
* Attendees: <br />
<br />
'''''Item 1'''''<br />
---------------------------------------<br />
*<br />
*<br />
*<br />
<br />
'''''Item 2'''''<br />
----------------------------------<br />
*<br />
*<br />
*<br />
<br />
'''''Item 3'''''<br />
-------------------<br />
*<br />
*<br />
*<br />
<br />
etc<br />
<br />
===Action Items===<br />
* TBD</div>Ivohttps://www.na-mic.org/w/index.php?title=Biositemaps&diff=38333Biositemaps2009-06-08T17:03:27Z<p>Ivo: replaced ivo's address with Image</p>
<hr />
<div>''' This is the main page for the NIH Roadmap National Centers for Biomedical Computing (NCBC) Working Group titled: Biositemaps and the Biomedical Resource Ontology (BRO) '''<br />
<br />
[[SDIWG:Software_and_Data_Integration_Working_Group|Top page of NCBC Working Groups web site]]<br />
<br />
Contacts for this Working Group are [http://www.loni.ucla.edu/~dinov/Dinov_Email.gif Ivo Dinov], [mailto:whetzel@stanford.edu Trish Whetzel], and [mailto:lysterp@mail.nih.gov Peter Lyster]<br />
<br />
For more information about the NCBCs visit the [http://www.ncbcs.org/ Top page of ncbcs.org web site which is maintained by the NCBCs themselves]<br />
<br />
----<br />
<br />
'''Biositemaps Project'''<br />
<br />
The Biositemaps Working Group of the [http://www.ncbcs.org/ NIH Roadmap National Centers of Biomedical Computing (NCBC) (www.ncbcs.org)] has developed a standard for communicating information on the Internet about biomedical resources (tools, data, software, material, and services). <b>The official public site of the Biositemaps Project is http://www.biositemaps.org/</b> In addition, the working group is using the biositemaps standard to address (i) locating, (ii) querying, (iii) composing or combining, and (iv) mining biomedical resources on the Internet. Each site which intends to contribute to the inventory instantiates a file on its Internet site ‘'biositemap.rdf' which conforms to a defined Information Model and uses concepts from the Biomedical Resource Ontology (BRO) describe the resources. Each biositemap.rdf file is simply a list of controlled metadata about resources that your organization uses or believes are important to biomedical research. <br />
<br />
* The key enabling technologies are the [http://www.ncbcs.org/biositemaps/formatDescription.html Information Model (IM)] which is the list of metadata fields about each resource (Resource_name, description, contact_person, resource_type,...) and <br />
* The [http://bioportal.bioontology.org/visualize/39977 Biomedical Resource Ontology (BRO) v2.7] which is a controlled terminology for the 'resource_type', 'area_of_research', and 'biomedical_activity' and which is used to improve the sensitivity and specificity of web searches. This is under development by a number of NIH-funded researchers who have a combined interest in classification of biomedical resources. The publication site for BRO is the BioPortal.<br />
<br />
----<br />
<br />
'''Current List of Biositemaps [[Feature_Requests | Feature Requests]]'''<br />
<br />
'''Current List of [[Search_Engines | Biositemaps Search Engines]]'''<br />
<br />
'''Current List of [[URLs | URLS that are used by Biositemaps Developers]]'''<br />
<br />
'''Current List of [[Developers_Meetings_and_Minutes | Developers Meetings and Minutes]]<br />
<br />
----<br />
<br />
'''[http://www.na-mic.org/Wiki/index.php/SDIWG:_NCBC_Resource_Yellow_Pages_and_Software_Ontologies Archive Biositemaps/Resourceome/Yellow Pages Development Pages]'''<br />
<br />
Site last updated: 20090607</div>Ivohttps://www.na-mic.org/w/index.php?title=SDIWG:Action_Items_20081219&diff=34918SDIWG:Action Items 200812192009-01-16T21:32:57Z<p>Ivo: </p>
<hr />
<div>Go back to top level of Resourcome working group discussion pages http://na-mic.org/Wiki/index.php/SDIWG:_NCBC_Resource_Yellow_Pages_and_Software_Ontologies<br />
<br />
Who: Natasha, Csongor, Ivo, Beth, Peter<br />
<br />
== Discussion and Action Items (2008-12-19): ==<br />
<br />
* What is minimum that is absolutely necessary? mechanism to publish: create form (auto-add to registry & email & widget for human-authentication)<br />
** Action: Natasha - weekly update of bioportal with latest biositemaps<br />
** Action: Ivo - weekly update of iTools already done<br />
** Action: Beth - <strike>document the fact that HTTP will inform last date/time of biositemaps file update</strike> (done)<br />
** Action: Beth - <strike>registration form for adding biositemaps to registry</strike> (done)<br />
** Action: Beth - Grep-like application against all biositemaps (Use Csongor's editor in browse only for presentation)<br />
** Action: Csongor - browseable mode for biositemaps editor<br />
<br />
* Do we have a good information model? Do we have good documentation?<br />
** Action: Someone (Natasha?) to email Joy at Stanford to review biositemap web site after above minimum requirements are met (e.g. here is where your current biositemap, how to view, update, etc.)<br />
<br />
* Note: Csongor back on January 8th<br />
<br />
* Note: Next meeting on 1-16-2008 (Beth to email reminder in January) <br />
<br />
== Outstanding action items: ==<br />
<br />
* Beth & Csongor: work on merging apis (complimentary functionality) upon his return from Australia (week of Dec. 15)<br />
** Csongor & I need to talk about this, but given all the editor work that is on Csongor's plate, I believe Michigan should be able to do this work <br />
<br />
* Csongor: Update Biositemaps Editor to allow invalid classes<br />
** Csongor, can this be done by end of January?<br />
<br />
* Beth & Peter: follow up with NCBC centers to publish & update biositemaps (note I2B2 & CCB use deprecated classes that need to be updated)<br />
** wait on this until other outstanding issues are completed <br />
** <strike>comment out deprecated classes for now</strike> (done)<br />
<br />
* Ivo: Update iTools application to consume new biositemaps RDF files via RDF-to-XML web service<br />
** Ivo/Natasha: Outstanding issues listed in followup email <br />
<br />
* There are problems with the database or bioportal that need to be resolved in order to expose NCBC resources on bioportal<br />
** Natasha: early January release should fix this<br />
<br />
* Beth: will clarify who will develop biositemaps search application following CTSA call regarding BRO/IM harmonizing<br />
** While we didn't get a chance to discuss this on the CTSA call, Michigan is willing to work on this with a target date early in 2009 (an exact date wouldn't be available until we can get our team to meet after the holidays).<br />
<br />
* Modify Biositemaps Editor to support multiple resource types<br />
** Csongor: to be done early next year (January 2009)<br />
<br />
* Modify Biositemaps Editor to support harmonized CTSA biositemaps information model:<br />
** Csongor: update editor<br />
** Question: Can Harpreet to write converter? <br />
<br />
* The expanded/harmonized biositemap has 25 possible properties which should be reviewed/trimmed down if possible <br />
** Byline will be dropped<br />
** Language and platform kept as optional<br />
** biositemap_author kept as optional (note that CTSA wants this not displayed in the editor -- they see it as a disincentive)<br />
<br />
* A significant outcome of the harmonizing call was the much broader definition of what is a Biomedical Resource that CTSA uses. Nancy and Harpreet were planning on following up with their proposed additions to the BRO first week of January<br />
<br />
==Biositemaps Web-Services Specifications==<br />
===I. Biomedical Resource Ontology (BRO) ontology=== <br />
* (http://bioportal.bioontology.org/virtual/1104). The following methods/functions will be valuable:<br />
** getBRO(): returns an XML with the complete current BRO hierarchy (starts with BRO root node)<br />
** getParents(BRONode): returns an XML with the meta-data of all the parents (in the BRO hierarchy), given BRONode. Most of the time there will be 1 parent, but there may be many<br />
** getChildren(BRONode): returns an XML with the meta-data of all the children (in the BRO hierarchy), given BRONode<br />
** getPartialBRO(BRONode): returns an XML with the meta-data of the BRO sub-hierarchy starting with BRONode<br />
** getSiblings(BRONode): returns an XML with the meta-data of all the siblings (in the BRO hierarchy) of the given BRONode (same hierarchy level)<br />
<br />
===II. Information Model (IM)===<br />
* http://www.ncbcs.org/biositemaps/formatDescription.html. The following methods/functions will be valuable:<br />
** getBiositemapsIM(): returns an XML with the meta-data of all the required/formal IM fields, their properties and descriptions. Like in: http://www.ncbcs.org/biositemaps/formatDescription.html<br />
** getBiositemapsIM_Property(int): returns an XML with the property-name of the IM field index by "int".<br />
** getBiositemapsIM_Description(int): returns an XML with the description of the provided IM field index by "int"<br />
** getBiositemapsIM_Description(property): returns an XML with the description of the provided IM property-name<br />
** getBiositemapsIM_Optional(property): returns an XML with the triples (name, property, value) of all non-standard, optional and non-core IM fields.<br />
<br />
===III. General Biositemaps.RDF web-service that provide not only the standard/required/IM meta-data, but any project/center/field- specific meta-data provided by the Biositemap creator/curator===<br />
: That is, we can have a center that has created a new Biositemap.RDF object, which contains the triple (name=NewField; property=NewProperty; value=NewValue). Suppose, "NewField" is *not* in the Biositemaps IM. We still need to provide services for people/ tools to retrieve this triple in XML, just like we allow retrieval of IM fields. This may be relatively easy, once we have the first two extensions (I. and II.).<br />
<br />
==[http://itools.ccb.ucla.edu/ iTools] processing (consumption/production) of Biositemaps.RDF==<br />
* Date: 01/14/09<br />
* Status of the current implementation of [http://itools.ccb.ucla.edu/ iTools] Yahoo-WebSearch of Biositemaps.RDF<br />
** [http://itools.ccb.ucla.edu/ iTools] WebSearch starts automatically every Friday morning. It may also be manually started by admins.<br />
** After the completion of the auto WebSearch, [http://itools.ccb.ucla.edu/ iTools] starts is own custom designed Web-Crawler, which traverses the entire http://www.biositemap.org/ domain and extracts all Biositemap.RDF objects there.<br />
** Finally [http://itools.ccb.ucla.edu/ iTools] combines both the Web-Search and the Web-Crawler results in the iTools SandBox. There are no identifiers indicating how was a Biositemaps.RDF object obtained (via web-search or web-crawling).<br />
* [http://itools.ccb.ucla.edu/ iTools] uses its own parser to parse Biositemap.RDF documents. There are 2 reasons for not using the [http://rest.bioontology.org/biositemap-server/parse?url=http://portal.ncibi.org/biositemap.rdf NCBO provided Biositemap.RDF web-service]:<br />
** The Biositemaps.XML genereated by this service does not provide a valid Biositemap.XML result (it's incompatible with the (legacy) Biositemaps.xml schema/format).<br />
** The RDF --> XML web-service converter only rewrites the RDF tags, so one needs yet another follow-up parser applied to the resulting XML object. Thus, the iTools client uses its own parser to minimize the overhead.<br />
* All Biositemaps.RDF clients (machines or humans), including [http://itools.ccb.ucla.edu/ iTools], will need an [http://www.ncbcs.org/biositemaps/formatDescription.html IM] parser web-service, as [[SDIWG:Action_Items_20081219#II._Information_Model_.28IM.29 | described above]].<br />
<br />
===Important Note===<br />
Note that in the new [http://www.ncbcs.org/biositemaps/formatDescription.html Biositemaps.RDF IM] there is no NCBC Center-name, which used to be a key tag in the old Biositemap.xml schema. This is now replaced by an [http://www.ncbcs.org/biositemaps/formatDescription.html Organization] tag. As a result of that, [http://itools.ccb.ucla.edu/ iTools] will not display NCBC-center-specific view in its tabular of graphical navigation panels.<br />
<br />
: ''BK: actually there is a center-name -- unfortunately the above IM is not alphabetically sorted, but the center property does exist along with organization.''<br />
<br />
: ''ID: Yes, 'center' it is defined by IM, but if you see this example http://rest.bioontology.org/biositemap-server/parse?url=http://portal.ncibi.org/biositemap.rdf, not all the resources have this field. If all resources are not guaranteed to have a clearly delineated center information, iTools will not be able to properly place these in the tabular/hyperbolic views.''<br />
<br />
==[[SDIWG:Action_Items_20090116| See Follow up notes]]==</div>Ivohttps://www.na-mic.org/w/index.php?title=SDIWG:Action_Items_20090116&diff=34917SDIWG:Action Items 200901162009-01-16T21:32:16Z<p>Ivo: </p>
<hr />
<div>Go back to top level of Resourcome working group discussion pages http://na-mic.org/Wiki/index.php/SDIWG:_NCBC_Resource_Yellow_Pages_and_Software_Ontologies<br />
<br />
'''Who''': Natasha, Ivo, Beth<br><br />
'''Background''': [[SDIWG:Action_Items_20081219| See meeting Notes of 12/19/2008]]<br />
<br />
== Discussion and Current Status (2009-01-16): ==<br />
* Natasha: BioPortal has been updated with latest biositemaps data<br />
* Ivo: iTools does a weekly reload of biositemaps (rdf/xml) found using Yahoo search engine (note this search only finds 2 biositemap files)<br />
* Beth: Biositemaps registration application is now available<br />
* All: Follow up via email on action items -- next meeting end of January or when (updated) Biositemaps Editor and Biositemaps Search applications are ready for review<br />
<br />
== Action Items (2009-01-16): ==<br />
* Csongor<br />
** Update Biositemaps Editor with the following by end of January:<br />
*** browse-mode<br />
*** allow invalid classes <br />
*** support multiple resource types <br />
*** support harmonized CTSA biositemaps information model (byline dropped, several other properties added, biositemap_author not displayed for CTSA)<br />
* Ivo<br />
** Send Natasha IATR biositemap.xml file to be translated to RDF (Done)<br />
** Update iTools to make use of biositemap registry and cease using XML biositemap files by January 23rd<br />
** Publish IATR and CCB biositemap file on UCLA/CCB server<br />
* Beth<br />
** Retire biositemap XML files from biositemaps.org web site once iTools has been updated to make use of biositemap registry<br />
** Forward proposed set of biositemap logos developed by UM graphic designer for consideration<br />
** Develop biositemaps search application based on BiositemapsConsumer prototype API described at https://appserver.ctaalliance.org/~bkirschn/biositemaps/ (initial release by end of January)<br />
** Work with Csongor to combine above BiositemapsConsumer API with existing BRO api (https://bmir-gforge.stanford.edu/gf/project/biositemaps/scmsvn/) <br />
* Natasha<br />
** Translate IATR biositemap.xml into biositemap.rdf format<br />
** Provide updated definition of available and proposed web services based on proposed list at bottom of [http://na-mic.org/Wiki/index.php/SDIWG:Action_Items_20081219|2008-12-19] discussion. Note that some of these services are already available, some can be developed, and some will not be developed (tabled pending further discussion)<br />
** Email Joy at Stanford to review biositemap web site after above minimum requirements are met (e.g. here is where your current biositemap, how to view, update, etc.) when above action items have been resolved<br />
* Peter<br />
** Follow up with other NCBC's requesting updated biositemap.rdf data once above action items have been resolved</div>Ivohttps://www.na-mic.org/w/index.php?title=SDIWG:Action_Items_20090116&diff=34916SDIWG:Action Items 200901162009-01-16T21:31:42Z<p>Ivo: </p>
<hr />
<div>Go back to top level of Resourcome working group discussion pages http://na-mic.org/Wiki/index.php/SDIWG:_NCBC_Resource_Yellow_Pages_and_Software_Ontologies<br />
<br />
'''Who''': Natasha, Ivo, Beth<br />
'''Background''': [[SDIWG:Action_Items_20081219| See meeting Notes of 12/19/2008]]<br />
<br />
== Discussion and Current Status (2009-01-16): ==<br />
* Natasha: BioPortal has been updated with latest biositemaps data<br />
* Ivo: iTools does a weekly reload of biositemaps (rdf/xml) found using Yahoo search engine (note this search only finds 2 biositemap files)<br />
* Beth: Biositemaps registration application is now available<br />
* All: Follow up via email on action items -- next meeting end of January or when (updated) Biositemaps Editor and Biositemaps Search applications are ready for review<br />
<br />
== Action Items (2009-01-16): ==<br />
* Csongor<br />
** Update Biositemaps Editor with the following by end of January:<br />
*** browse-mode<br />
*** allow invalid classes <br />
*** support multiple resource types <br />
*** support harmonized CTSA biositemaps information model (byline dropped, several other properties added, biositemap_author not displayed for CTSA)<br />
* Ivo<br />
** Send Natasha IATR biositemap.xml file to be translated to RDF (Done)<br />
** Update iTools to make use of biositemap registry and cease using XML biositemap files by January 23rd<br />
** Publish IATR and CCB biositemap file on UCLA/CCB server<br />
* Beth<br />
** Retire biositemap XML files from biositemaps.org web site once iTools has been updated to make use of biositemap registry<br />
** Forward proposed set of biositemap logos developed by UM graphic designer for consideration<br />
** Develop biositemaps search application based on BiositemapsConsumer prototype API described at https://appserver.ctaalliance.org/~bkirschn/biositemaps/ (initial release by end of January)<br />
** Work with Csongor to combine above BiositemapsConsumer API with existing BRO api (https://bmir-gforge.stanford.edu/gf/project/biositemaps/scmsvn/) <br />
* Natasha<br />
** Translate IATR biositemap.xml into biositemap.rdf format<br />
** Provide updated definition of available and proposed web services based on proposed list at bottom of [http://na-mic.org/Wiki/index.php/SDIWG:Action_Items_20081219|2008-12-19] discussion. Note that some of these services are already available, some can be developed, and some will not be developed (tabled pending further discussion)<br />
** Email Joy at Stanford to review biositemap web site after above minimum requirements are met (e.g. here is where your current biositemap, how to view, update, etc.) when above action items have been resolved<br />
* Peter<br />
** Follow up with other NCBC's requesting updated biositemap.rdf data once above action items have been resolved</div>Ivohttps://www.na-mic.org/w/index.php?title=SDIWG:Action_Items_20081219&diff=34909SDIWG:Action Items 200812192009-01-16T19:01:12Z<p>Ivo: /* Important Note */</p>
<hr />
<div>Go back to top level of Resourcome working group discussion pages http://na-mic.org/Wiki/index.php/SDIWG:_NCBC_Resource_Yellow_Pages_and_Software_Ontologies<br />
<br />
Who: Natasha, Csongor, Ivo, Beth, Peter<br />
<br />
== Discussion and Action Items (2008-12-19): ==<br />
<br />
* What is minimum that is absolutely necessary? mechanism to publish: create form (auto-add to registry & email & widget for human-authentication)<br />
** Action: Natasha - weekly update of bioportal with latest biositemaps<br />
** Action: Ivo - weekly update of iTools already done<br />
** Action: Beth - <strike>document the fact that HTTP will inform last date/time of biositemaps file update</strike> (done)<br />
** Action: Beth - registration form for adding biositemaps to registry<br />
** Action: Beth - Grep-like application against all biositemaps (Use Csongor's editor in browse only for presentation)<br />
** Action: Csongor - browseable mode for biositemaps editor<br />
<br />
* Do we have a good information model? Do we have good documentation?<br />
** Action: Someone (Natasha?) to email Joy at Stanford to review biositemap web site after above minimum requirements are met (e.g. here is where your current biositemap, how to view, update, etc.)<br />
<br />
* Note: Csongor back on January 8th<br />
<br />
* Note: Next meeting on 1-16-2008 (Beth to email reminder in January) <br />
<br />
== Outstanding action items: ==<br />
<br />
* Beth & Csongor: work on merging apis (complimentary functionality) upon his return from Australia (week of Dec. 15)<br />
** Csongor & I need to talk about this, but given all the editor work that is on Csongor's plate, I believe Michigan should be able to do this work <br />
<br />
* Csongor: Update Biositemaps Editor to allow invalid classes<br />
** Csongor, can this be done by end of January?<br />
<br />
* Beth & Peter: follow up with NCBC centers to publish & update biositemaps (note I2B2 & CCB use deprecated classes that need to be updated)<br />
** wait on this until other outstanding issues are completed <br />
** <strike>comment out deprecated classes for now</strike> (done)<br />
<br />
* Ivo: Update iTools application to consume new biositemaps RDF files via RDF-to-XML web service<br />
** Ivo/Natasha: Outstanding issues listed in followup email <br />
<br />
* There are problems with the database or bioportal that need to be resolved in order to expose NCBC resources on bioportal<br />
** Natasha: early January release should fix this<br />
<br />
* Beth: will clarify who will develop biositemaps search application following CTSA call regarding BRO/IM harmonizing<br />
** While we didn't get a chance to discuss this on the CTSA call, Michigan is willing to work on this with a target date early in 2009 (an exact date wouldn't be available until we can get our team to meet after the holidays).<br />
<br />
* Modify Biositemaps Editor to support multiple resource types<br />
** Csongor: to be done early next year (January 2009)<br />
<br />
* Modify Biositemaps Editor to support harmonized CTSA biositemaps information model:<br />
** Csongor: update editor<br />
** Question: Can Harpreet to write converter? <br />
<br />
* The expanded/harmonized biositemap has 25 possible properties which should be reviewed/trimmed down if possible <br />
** Byline will be dropped<br />
** Language and platform kept as optional<br />
** biositemap_author kept as optional (note that CTSA wants this not displayed in the editor -- they see it as a disincentive)<br />
<br />
* A significant outcome of the harmonizing call was the much broader definition of what is a Biomedical Resource that CTSA uses. Nancy and Harpreet were planning on following up with their proposed additions to the BRO first week of January<br />
<br />
==Biositemaps Web-Services Specifications==<br />
===I. Biomedical Resource Ontology (BRO) ontology=== <br />
* (http://bioportal.bioontology.org/virtual/1104). The following methods/functions will be valuable:<br />
** getBRO(): returns an XML with the complete current BRO hierarchy (starts with BRO root node)<br />
** getParents(BRONode): returns an XML with the meta-data of all the parents (in the BRO hierarchy), given BRONode. Most of the time there will be 1 parent, but there may be many<br />
** getChildren(BRONode): returns an XML with the meta-data of all the children (in the BRO hierarchy), given BRONode<br />
** getPartialBRO(BRONode): returns an XML with the meta-data of the BRO sub-hierarchy starting with BRONode<br />
** getSiblings(BRONode): returns an XML with the meta-data of all the siblings (in the BRO hierarchy) of the given BRONode (same hierarchy level)<br />
<br />
===II. Information Model (IM)===<br />
* http://www.ncbcs.org/biositemaps/formatDescription.html. The following methods/functions will be valuable:<br />
** getBiositemapsIM(): returns an XML with the meta-data of all the required/formal IM fields, their properties and descriptions. Like in: http://www.ncbcs.org/biositemaps/formatDescription.html<br />
** getBiositemapsIM_Property(int): returns an XML with the property-name of the IM field index by "int".<br />
** getBiositemapsIM_Description(int): returns an XML with the description of the provided IM field index by "int"<br />
** getBiositemapsIM_Description(property): returns an XML with the description of the provided IM property-name<br />
** getBiositemapsIM_Optional(property): returns an XML with the triples (name, property, value) of all non-standard, optional and non-core IM fields.<br />
<br />
===III. General Biositemaps.RDF web-service that provide not only the standard/required/IM meta-data, but any project/center/field- specific meta-data provided by the Biositemap creator/curator===<br />
: That is, we can have a center that has created a new Biositemap.RDF object, which contains the triple (name=NewField; property=NewProperty; value=NewValue). Suppose, "NewField" is *not* in the Biositemaps IM. We still need to provide services for people/ tools to retrieve this triple in XML, just like we allow retrieval of IM fields. This may be relatively easy, once we have the first two extensions (I. and II.).<br />
<br />
==[http://itools.ccb.ucla.edu/ iTools] processing (consumption/production) of Biositemaps.RDF==<br />
* Date: 01/14/09<br />
* Status of the current implementation of [http://itools.ccb.ucla.edu/ iTools] Yahoo-WebSearch of Biositemaps.RDF<br />
** [http://itools.ccb.ucla.edu/ iTools] WebSearch starts automatically every Friday morning. It may also be manually started by admins.<br />
** After the completion of the auto WebSearch, [http://itools.ccb.ucla.edu/ iTools] starts is own custom designed Web-Crawler, which traverses the entire http://www.biositemap.org/ domain and extracts all Biositemap.RDF objects there.<br />
** Finally [http://itools.ccb.ucla.edu/ iTools] combines both the Web-Search and the Web-Crawler results in the iTools SandBox. There are no identifiers indicating how was a Biositemaps.RDF object obtained (via web-search or web-crawling).<br />
* [http://itools.ccb.ucla.edu/ iTools] uses its own parser to parse Biositemap.RDF documents. There are 2 reasons for not using the [http://rest.bioontology.org/biositemap-server/parse?url=http://portal.ncibi.org/biositemap.rdf NCBO provided Biositemap.RDF web-service]:<br />
** The Biositemaps.XML genereated by this service does not provide a valid Biositemap.XML result (it's incompatible with the (legacy) Biositemaps.xml schema/format).<br />
** The RDF --> XML web-service converter only rewrites the RDF tags, so one needs yet another follow-up parser applied to the resulting XML object. Thus, the iTools client uses its own parser to minimize the overhead.<br />
* All Biositemaps.RDF clients (machines or humans), including [http://itools.ccb.ucla.edu/ iTools], will need an [http://www.ncbcs.org/biositemaps/formatDescription.html IM] parser web-service, as [[SDIWG:Action_Items_20081219#II._Information_Model_.28IM.29 | described above]].<br />
<br />
===Important Note===<br />
Note that in the new [http://www.ncbcs.org/biositemaps/formatDescription.html Biositemaps.RDF IM] there is no NCBC Center-name, which used to be a key tag in the old Biositemap.xml schema. This is now replaced by an [http://www.ncbcs.org/biositemaps/formatDescription.html Organization] tag. As a result of that, [http://itools.ccb.ucla.edu/ iTools] will not display NCBC-center-specific view in its tabular of graphical navigation panels.<br />
<br />
: ''BK: actually there is a center-name -- unfortunately the above IM is not alphabetically sorted, but the center property does exist along with organization.''<br />
<br />
: ''ID: Yes, 'center' it is defined by IM, but if you see this example http://rest.bioontology.org/biositemap-server/parse?url=http://portal.ncibi.org/biositemap.rdf, not all the resources have this field. If all resources are not guaranteed to have a clearly delineated center information, iTools will not be able to properly place these in the tabular/hyperbolic views.''</div>Ivohttps://www.na-mic.org/w/index.php?title=SDIWG:Action_Items_20081219&diff=34905SDIWG:Action Items 200812192009-01-16T18:25:43Z<p>Ivo: </p>
<hr />
<div>Go back to top level of Resourcome working group discussion pages http://na-mic.org/Wiki/index.php/SDIWG:_NCBC_Resource_Yellow_Pages_and_Software_Ontologies<br />
<br />
Who: Natasha, Csongor, Ivo, Beth, Peter<br />
<br />
== Discussion and Action Items (2008-12-19): ==<br />
<br />
* What is minimum that is absolutely necessary? mechanism to publish: create form (auto-add to registry & email & widget for human-authentication)<br />
** Action: Natasha - weekly update of bioportal with latest biositemaps<br />
** Action: Ivo - weekly update of iTools already done<br />
** Action: Beth - <strike>document the fact that HTTP will inform last date/time of biositemaps file update</strike> (done)<br />
** Action: Beth - registration form for adding biositemaps to registry<br />
** Action: Beth - Grep-like application against all biositemaps (Use Csongor's editor in browse only for presentation)<br />
** Action: Csongor - browseable mode for biositemaps editor<br />
<br />
* Do we have a good information model? Do we have good documentation?<br />
** Action: Someone (Natasha?) to email Joy at Stanford to review biositemap web site after above minimum requirements are met (e.g. here is where your current biositemap, how to view, update, etc.)<br />
<br />
* Note: Csongor back on January 8th<br />
<br />
* Note: Next meeting on 1-16-2008 (Beth to email reminder in January) <br />
<br />
== Outstanding action items: ==<br />
<br />
* Beth & Csongor: work on merging apis (complimentary functionality) upon his return from Australia (week of Dec. 15)<br />
** Csongor & I need to talk about this, but given all the editor work that is on Csongor's plate, I believe Michigan should be able to do this work <br />
<br />
* Csongor: Update Biositemaps Editor to allow invalid classes<br />
** Csongor, can this be done by end of January?<br />
<br />
* Beth & Peter: follow up with NCBC centers to publish & update biositemaps (note I2B2 & CCB use deprecated classes that need to be updated)<br />
** wait on this until other outstanding issues are completed <br />
** <strike>comment out deprecated classes for now</strike> (done)<br />
<br />
* Ivo: Update iTools application to consume new biositemaps RDF files via RDF-to-XML web service<br />
** Ivo/Natasha: Outstanding issues listed in followup email <br />
<br />
* There are problems with the database or bioportal that need to be resolved in order to expose NCBC resources on bioportal<br />
** Natasha: early January release should fix this<br />
<br />
* Beth: will clarify who will develop biositemaps search application following CTSA call regarding BRO/IM harmonizing<br />
** While we didn't get a chance to discuss this on the CTSA call, Michigan is willing to work on this with a target date early in 2009 (an exact date wouldn't be available until we can get our team to meet after the holidays).<br />
<br />
* Modify Biositemaps Editor to support multiple resource types<br />
** Csongor: to be done early next year (January 2009)<br />
<br />
* Modify Biositemaps Editor to support harmonized CTSA biositemaps information model:<br />
** Csongor: update editor<br />
** Question: Can Harpreet to write converter? <br />
<br />
* The expanded/harmonized biositemap has 25 possible properties which should be reviewed/trimmed down if possible <br />
** Byline will be dropped<br />
** Language and platform kept as optional<br />
** biositemap_author kept as optional (note that CTSA wants this not displayed in the editor -- they see it as a disincentive)<br />
<br />
* A significant outcome of the harmonizing call was the much broader definition of what is a Biomedical Resource that CTSA uses. Nancy and Harpreet were planning on following up with their proposed additions to the BRO first week of January<br />
<br />
==Biositemaps Web-Services Specifications==<br />
===I. Biomedical Resource Ontology (BRO) ontology=== <br />
* (http://bioportal.bioontology.org/virtual/1104). The following methods/functions will be valuable:<br />
** getBRO(): returns an XML with the complete current BRO hierarchy (starts with BRO root node)<br />
** getParents(BRONode): returns an XML with the meta-data of all the parents (in the BRO hierarchy), given BRONode. Most of the time there will be 1 parent, but there may be many<br />
** getChildren(BRONode): returns an XML with the meta-data of all the children (in the BRO hierarchy), given BRONode<br />
** getPartialBRO(BRONode): returns an XML with the meta-data of the BRO sub-hierarchy starting with BRONode<br />
** getSiblings(BRONode): returns an XML with the meta-data of all the siblings (in the BRO hierarchy) of the given BRONode (same hierarchy level)<br />
<br />
===II. Information Model (IM)===<br />
* http://www.ncbcs.org/biositemaps/formatDescription.html. The following methods/functions will be valuable:<br />
** getBiositemapsIM(): returns an XML with the meta-data of all the required/formal IM fields, their properties and descriptions. Like in: http://www.ncbcs.org/biositemaps/formatDescription.html<br />
** getBiositemapsIM_Property(int): returns an XML with the property-name of the IM field index by "int".<br />
** getBiositemapsIM_Description(int): returns an XML with the description of the provided IM field index by "int"<br />
** getBiositemapsIM_Description(property): returns an XML with the description of the provided IM property-name<br />
** getBiositemapsIM_Optional(property): returns an XML with the triples (name, property, value) of all non-standard, optional and non-core IM fields.<br />
<br />
===III. General Biositemaps.RDF web-service that provide not only the standard/required/IM meta-data, but any project/center/field- specific meta-data provided by the Biositemap creator/curator===<br />
: That is, we can have a center that has created a new Biositemap.RDF object, which contains the triple (name=NewField; property=NewProperty; value=NewValue). Suppose, "NewField" is *not* in the Biositemaps IM. We still need to provide services for people/ tools to retrieve this triple in XML, just like we allow retrieval of IM fields. This may be relatively easy, once we have the first two extensions (I. and II.).<br />
<br />
==[http://itools.ccb.ucla.edu/ iTools] processing (consumption/production) of Biositemaps.RDF==<br />
* Date: 01/14/09<br />
* Status of the current implementation of [http://itools.ccb.ucla.edu/ iTools] Yahoo-WebSearch of Biositemaps.RDF<br />
** [http://itools.ccb.ucla.edu/ iTools] WebSearch starts automatically every Friday morning. It may also be manually started by admins.<br />
** After the completion of the auto WebSearch, [http://itools.ccb.ucla.edu/ iTools] starts is own custom designed Web-Crawler, which traverses the entire http://www.biositemap.org/ domain and extracts all Biositemap.RDF objects there.<br />
** Finally [http://itools.ccb.ucla.edu/ iTools] combines both the Web-Search and the Web-Crawler results in the iTools SandBox. There are no identifiers indicating how was a Biositemaps.RDF object obtained (via web-search or web-crawling).<br />
* [http://itools.ccb.ucla.edu/ iTools] uses its own parser to parse Biositemap.RDF documents. There are 2 reasons for not using the [http://rest.bioontology.org/biositemap-server/parse?url=http://portal.ncibi.org/biositemap.rdf NCBO provided Biositemap.RDF web-service]:<br />
** The Biositemaps.XML genereated by this service does not provide a valid Biositemap.XML result (it's incompatible with the (legacy) Biositemaps.xml schema/format).<br />
** The RDF --> XML web-service converter only rewrites the RDF tags, so one needs yet another follow-up parser applied to the resulting XML object. Thus, the iTools client uses its own parser to minimize the overhead.<br />
* All Biositemaps.RDF clients (machines or humans), including [http://itools.ccb.ucla.edu/ iTools], will need an [http://www.ncbcs.org/biositemaps/formatDescription.html IM] parser web-service, as [[SDIWG:Action_Items_20081219#II._Information_Model_.28IM.29 | described above]].<br />
<br />
===Important Note===<br />
Note that in the new [http://www.ncbcs.org/biositemaps/formatDescription.html Biositemaps.RDF IM] there is no NCBC Center-name, which used to be a key tag in the old Biositemap.xml schema. This is now replaced by an [http://www.ncbcs.org/biositemaps/formatDescription.html Organization] tag. As a result of that, [http://itools.ccb.ucla.edu/ iTools] will not display NCBC-center-specific view in its tabular of graphical navigation panels.<br />
<br />
: ''BK: actually there is a center-name -- unfortunately the above IM is not alphabetically sorted, but the center property does exist along with organization.''<br />
<br />
: ''ID: Yes, 'center' it is defined by IM, but if you see this example<br />
http://rest.bioontology.org/biositemap-server/parse?url=http://portal.ncibi.org/biositemap.rdf, not all the resources have this field. If all resources are not guaranteed to have a clearly delineated center information, iTools will not be able to properly place these in the tabular/hyperbolic views.''</div>Ivohttps://www.na-mic.org/w/index.php?title=SDIWG:Action_Items_20081219&diff=34868SDIWG:Action Items 200812192009-01-14T23:54:53Z<p>Ivo: /* iTools processing (consumption/production) of Biositemaps.RDF */</p>
<hr />
<div>Go back to top level of Resourcome working group discussion pages http://na-mic.org/Wiki/index.php/SDIWG:_NCBC_Resource_Yellow_Pages_and_Software_Ontologies<br />
<br />
Who: Natasha, Csongor, Ivo, Beth, Peter<br />
<br />
== Discussion and Action Items (2008-12-19): ==<br />
<br />
* What is minimum that is absolutely necessary? mechanism to publish: create form (auto-add to registry & email & widget for human-authentication)<br />
** Action: Natasha - weekly update of bioportal with latest biositemaps<br />
** Action: Ivo - weekly update of iTools already done<br />
** Action: Beth - <strike>document the fact that HTTP will inform last date/time of biositemaps file update</strike> (done)<br />
** Action: Beth - registration form for adding biositemaps to registry<br />
** Action: Beth - Grep-like application against all biositemaps (Use Csongor's editor in browse only for presentation)<br />
** Action: Csongor - browseable mode for biositemaps editor<br />
<br />
* Do we have a good information model? Do we have good documentation?<br />
** Action: Someone (Natasha?) to email Joy at Stanford to review biositemap web site after above minimum requirements are met (e.g. here is where your current biositemap, how to view, update, etc.)<br />
<br />
* Note: Csongor back on January 8th<br />
<br />
* Note: Next meeting on 1-16-2008 (Beth to email reminder in January) <br />
<br />
== Outstanding action items: ==<br />
<br />
* Beth & Csongor: work on merging apis (complimentary functionality) upon his return from Australia (week of Dec. 15)<br />
** Csongor & I need to talk about this, but given all the editor work that is on Csongor's plate, I believe Michigan should be able to do this work <br />
<br />
* Csongor: Update Biositemaps Editor to allow invalid classes<br />
** Csongor, can this be done by end of January?<br />
<br />
* Beth & Peter: follow up with NCBC centers to publish & update biositemaps (note I2B2 & CCB use deprecated classes that need to be updated)<br />
** wait on this until other outstanding issues are completed <br />
** <strike>comment out deprecated classes for now</strike> (done)<br />
<br />
* Ivo: Update iTools application to consume new biositemaps RDF files via RDF-to-XML web service<br />
** Ivo/Natasha: Outstanding issues listed in followup email <br />
<br />
* There are problems with the database or bioportal that need to be resolved in order to expose NCBC resources on bioportal<br />
** Natasha: early January release should fix this<br />
<br />
* Beth: will clarify who will develop biositemaps search application following CTSA call regarding BRO/IM harmonizing<br />
** While we didn't get a chance to discuss this on the CTSA call, Michigan is willing to work on this with a target date early in 2009 (an exact date wouldn't be available until we can get our team to meet after the holidays).<br />
<br />
* Modify Biositemaps Editor to support multiple resource types<br />
** Csongor: to be done early next year (January 2009)<br />
<br />
* Modify Biositemaps Editor to support harmonized CTSA biositemaps information model:<br />
** Csongor: update editor<br />
** Question: Can Harpreet to write converter? <br />
<br />
* The expanded/harmonized biositemap has 25 possible properties which should be reviewed/trimmed down if possible <br />
** Byline will be dropped<br />
** Language and platform kept as optional<br />
** biositemap_author kept as optional (note that CTSA wants this not displayed in the editor -- they see it as a disincentive)<br />
<br />
* A significant outcome of the harmonizing call was the much broader definition of what is a Biomedical Resource that CTSA uses. Nancy and Harpreet were planning on following up with their proposed additions to the BRO first week of January<br />
<br />
==Biositemaps Web-Services Specifications==<br />
===I. Biomedical Resource Ontology (BRO) ontology=== <br />
* (http://bioportal.bioontology.org/virtual/1104). The following methods/functions will be valuable:<br />
** getBRO(): returns an XML with the complete current BRO hierarchy (starts with BRO root node)<br />
** getParents(BRONode): returns an XML with the meta-data of all the parents (in the BRO hierarchy), given BRONode. Most of the time there will be 1 parent, but there may be many<br />
** getChildren(BRONode): returns an XML with the meta-data of all the children (in the BRO hierarchy), given BRONode<br />
** getPartialBRO(BRONode): returns an XML with the meta-data of the BRO sub-hierarchy starting with BRONode<br />
** getSiblings(BRONode): returns an XML with the meta-data of all the siblings (in the BRO hierarchy) of the given BRONode (same hierarchy level)<br />
<br />
===II. Information Model (IM)===<br />
* http://www.ncbcs.org/biositemaps/formatDescription.html. The following methods/functions will be valuable:<br />
** getBiositemapsIM(): returns an XML with the meta-data of all the required/formal IM fields, their properties and descriptions. Like in: http://www.ncbcs.org/biositemaps/formatDescription.html<br />
** getBiositemapsIM_Property(int): returns an XML with the property-name of the IM field index by "int".<br />
** getBiositemapsIM_Description(int): returns an XML with the description of the provided IM field index by "int"<br />
** getBiositemapsIM_Description(property): returns an XML with the description of the provided IM property-name<br />
** getBiositemapsIM_Optional(property): returns an XML with the triples (name, property, value) of all non-standard, optional and non-core IM fields.<br />
<br />
===III. General Biositemaps.RDF web-service that provide not only the standard/required/IM meta-data, but any project/center/field- specific meta-data provided by the Biositemap creator/curator===<br />
: That is, we can have a center that has created a new Biositemap.RDF object, which contains the triple (name=NewField; property=NewProperty; value=NewValue). Suppose, "NewField" is *not* in the Biositemaps IM. We still need to provide services for people/ tools to retrieve this triple in XML, just like we allow retrieval of IM fields. This may be relatively easy, once we have the first two extensions (I. and II.).<br />
<br />
==[http://itools.ccb.ucla.edu/ iTools] processing (consumption/production) of Biositemaps.RDF==<br />
* Date: 01/14/09<br />
* Status of the current implementation of [http://itools.ccb.ucla.edu/ iTools] Yahoo-WebSearch of Biositemaps.RDF<br />
** [http://itools.ccb.ucla.edu/ iTools] WebSearch starts automatically every Friday morning. It may also be manually started by admins.<br />
** After the completion of the auto WebSearch, [http://itools.ccb.ucla.edu/ iTools] starts is own custom designed Web-Crawler, which traverses the entire http://www.biositemap.org/ domain and extracts all Biositemap.RDF objects there.<br />
** Finally [http://itools.ccb.ucla.edu/ iTools] combines both the Web-Search and the Web-Crawler results in the iTools SandBox. There are no identifiers indicating how was a Biositemaps.RDF object obtained (via web-search or web-crawling).<br />
* [http://itools.ccb.ucla.edu/ iTools] uses its own parser to parse Biositemap.RDF documents. There are 2 reasons for not using the [http://rest.bioontology.org/biositemap-server/parse?url=http://portal.ncibi.org/biositemap.rdf NCBO provided Biositemap.RDF web-service]:<br />
** The Biositemaps.XML genereated by this service does not provide a valid Biositemap.XML result (it's incompatible with the (legacy) Biositemaps.xml schema/format).<br />
** The RDF --> XML web-service converter only rewrites the RDF tags, so one needs yet another follow-up parser applied to the resulting XML object. Thus, the iTools client uses its own parser to minimize the overhead.<br />
* All Biositemaps.RDF clients (machines or humans), including [http://itools.ccb.ucla.edu/ iTools], will need an [http://www.ncbcs.org/biositemaps/formatDescription.html IM] parser web-service, as [[SDIWG:Action_Items_20081219#II._Information_Model_.28IM.29 | described above]].<br />
<br />
===Important Note===<br />
Note that in the new [http://www.ncbcs.org/biositemaps/formatDescription.html Biositemaps.RDF IM] there is no NCBC Center-name, which used to be a key tag in the old Biositemap.xml schema. This is now replaced by an [http://www.ncbcs.org/biositemaps/formatDescription.html Organization] tag. As a result of that, [http://itools.ccb.ucla.edu/ iTools] will not display NCBC-center-specific view in its tabular of graphical navigation panels.</div>Ivohttps://www.na-mic.org/w/index.php?title=SDIWG:Action_Items_20081219&diff=34867SDIWG:Action Items 200812192009-01-14T23:54:05Z<p>Ivo: /* iTools processing (consumption/production) of Biositemaps.RDF */</p>
<hr />
<div>Go back to top level of Resourcome working group discussion pages http://na-mic.org/Wiki/index.php/SDIWG:_NCBC_Resource_Yellow_Pages_and_Software_Ontologies<br />
<br />
Who: Natasha, Csongor, Ivo, Beth, Peter<br />
<br />
== Discussion and Action Items (2008-12-19): ==<br />
<br />
* What is minimum that is absolutely necessary? mechanism to publish: create form (auto-add to registry & email & widget for human-authentication)<br />
** Action: Natasha - weekly update of bioportal with latest biositemaps<br />
** Action: Ivo - weekly update of iTools already done<br />
** Action: Beth - <strike>document the fact that HTTP will inform last date/time of biositemaps file update</strike> (done)<br />
** Action: Beth - registration form for adding biositemaps to registry<br />
** Action: Beth - Grep-like application against all biositemaps (Use Csongor's editor in browse only for presentation)<br />
** Action: Csongor - browseable mode for biositemaps editor<br />
<br />
* Do we have a good information model? Do we have good documentation?<br />
** Action: Someone (Natasha?) to email Joy at Stanford to review biositemap web site after above minimum requirements are met (e.g. here is where your current biositemap, how to view, update, etc.)<br />
<br />
* Note: Csongor back on January 8th<br />
<br />
* Note: Next meeting on 1-16-2008 (Beth to email reminder in January) <br />
<br />
== Outstanding action items: ==<br />
<br />
* Beth & Csongor: work on merging apis (complimentary functionality) upon his return from Australia (week of Dec. 15)<br />
** Csongor & I need to talk about this, but given all the editor work that is on Csongor's plate, I believe Michigan should be able to do this work <br />
<br />
* Csongor: Update Biositemaps Editor to allow invalid classes<br />
** Csongor, can this be done by end of January?<br />
<br />
* Beth & Peter: follow up with NCBC centers to publish & update biositemaps (note I2B2 & CCB use deprecated classes that need to be updated)<br />
** wait on this until other outstanding issues are completed <br />
** <strike>comment out deprecated classes for now</strike> (done)<br />
<br />
* Ivo: Update iTools application to consume new biositemaps RDF files via RDF-to-XML web service<br />
** Ivo/Natasha: Outstanding issues listed in followup email <br />
<br />
* There are problems with the database or bioportal that need to be resolved in order to expose NCBC resources on bioportal<br />
** Natasha: early January release should fix this<br />
<br />
* Beth: will clarify who will develop biositemaps search application following CTSA call regarding BRO/IM harmonizing<br />
** While we didn't get a chance to discuss this on the CTSA call, Michigan is willing to work on this with a target date early in 2009 (an exact date wouldn't be available until we can get our team to meet after the holidays).<br />
<br />
* Modify Biositemaps Editor to support multiple resource types<br />
** Csongor: to be done early next year (January 2009)<br />
<br />
* Modify Biositemaps Editor to support harmonized CTSA biositemaps information model:<br />
** Csongor: update editor<br />
** Question: Can Harpreet to write converter? <br />
<br />
* The expanded/harmonized biositemap has 25 possible properties which should be reviewed/trimmed down if possible <br />
** Byline will be dropped<br />
** Language and platform kept as optional<br />
** biositemap_author kept as optional (note that CTSA wants this not displayed in the editor -- they see it as a disincentive)<br />
<br />
* A significant outcome of the harmonizing call was the much broader definition of what is a Biomedical Resource that CTSA uses. Nancy and Harpreet were planning on following up with their proposed additions to the BRO first week of January<br />
<br />
==Biositemaps Web-Services Specifications==<br />
===I. Biomedical Resource Ontology (BRO) ontology=== <br />
* (http://bioportal.bioontology.org/virtual/1104). The following methods/functions will be valuable:<br />
** getBRO(): returns an XML with the complete current BRO hierarchy (starts with BRO root node)<br />
** getParents(BRONode): returns an XML with the meta-data of all the parents (in the BRO hierarchy), given BRONode. Most of the time there will be 1 parent, but there may be many<br />
** getChildren(BRONode): returns an XML with the meta-data of all the children (in the BRO hierarchy), given BRONode<br />
** getPartialBRO(BRONode): returns an XML with the meta-data of the BRO sub-hierarchy starting with BRONode<br />
** getSiblings(BRONode): returns an XML with the meta-data of all the siblings (in the BRO hierarchy) of the given BRONode (same hierarchy level)<br />
<br />
===II. Information Model (IM)===<br />
* http://www.ncbcs.org/biositemaps/formatDescription.html. The following methods/functions will be valuable:<br />
** getBiositemapsIM(): returns an XML with the meta-data of all the required/formal IM fields, their properties and descriptions. Like in: http://www.ncbcs.org/biositemaps/formatDescription.html<br />
** getBiositemapsIM_Property(int): returns an XML with the property-name of the IM field index by "int".<br />
** getBiositemapsIM_Description(int): returns an XML with the description of the provided IM field index by "int"<br />
** getBiositemapsIM_Description(property): returns an XML with the description of the provided IM property-name<br />
** getBiositemapsIM_Optional(property): returns an XML with the triples (name, property, value) of all non-standard, optional and non-core IM fields.<br />
<br />
===III. General Biositemaps.RDF web-service that provide not only the standard/required/IM meta-data, but any project/center/field- specific meta-data provided by the Biositemap creator/curator===<br />
: That is, we can have a center that has created a new Biositemap.RDF object, which contains the triple (name=NewField; property=NewProperty; value=NewValue). Suppose, "NewField" is *not* in the Biositemaps IM. We still need to provide services for people/ tools to retrieve this triple in XML, just like we allow retrieval of IM fields. This may be relatively easy, once we have the first two extensions (I. and II.).<br />
<br />
==[http://itools.ccb.ucla.edu/ iTools] processing (consumption/production) of Biositemaps.RDF==<br />
* Date: 01/14/09<br />
* Status of the current implementation of [http://itools.ccb.ucla.edu/ iTools] Yahoo-WebSearch of Biositemaps.RDF<br />
** [http://itools.ccb.ucla.edu/ iTools] WebSearch starts automatically every Friday morning. It may also be manually started by admins.<br />
** After the completion of the auto WebSearch, [http://itools.ccb.ucla.edu/ iTools] starts is own custom designed Web-Crawler, which traverses the entire http://www.biositemap.org/ domain and extracts all Biositemap.RDF objects there.<br />
** Finally [http://itools.ccb.ucla.edu/ iTools] combines both the Web-Search and the Web-Crawler results in the iTools SandBox. There are no identifiers indicating how was a Biositemaps.RDF object obtained (via web-search or web-crawling).<br />
* [http://itools.ccb.ucla.edu/ iTools] uses its own parser to parse Biositemap.RDF documents. There are 2 reasons for not using the [http://rest.bioontology.org/biositemap-server/parse?url=http://portal.ncibi.org/biositemap.rdf NCBO provided Biositemap.RDF web-service]:<br />
** The Biositemaps.XML genereated by this service does not provide a valid Biositemap.XML result (it's incompatible with the (legacy) Biositemaps.xml schema/format).<br />
** The RDF --> XML web-service converter only rewrites the RDF tags, so one needs yet another follow-up parser applied to the resulting XML object. Thus, the iTools client uses its own parser to minimize the overhead.<br />
* All Biositemaps.RDF clients (machines or humans), including [http://itools.ccb.ucla.edu/ iTools], will need an [http://www.ncbcs.org/biositemaps/formatDescription.html IM] parser web-service, as described above.<br />
<br />
===Important Note===<br />
Note that in the new [http://www.ncbcs.org/biositemaps/formatDescription.html Biositemaps.RDF IM] there is no NCBC Center-name, which used to be a key tag in the old Biositemap.xml schema. This is now replaced by an [http://www.ncbcs.org/biositemaps/formatDescription.html Organization] tag. As a result of that, [http://itools.ccb.ucla.edu/ iTools] will not display NCBC-center-specific view in its tabular of graphical navigation panels.</div>Ivohttps://www.na-mic.org/w/index.php?title=SDIWG:Action_Items_20081219&diff=34866SDIWG:Action Items 200812192009-01-14T23:51:37Z<p>Ivo: /* iTools processing (consumption/production) of Biositemaps.RDF */</p>
<hr />
<div>Go back to top level of Resourcome working group discussion pages http://na-mic.org/Wiki/index.php/SDIWG:_NCBC_Resource_Yellow_Pages_and_Software_Ontologies<br />
<br />
Who: Natasha, Csongor, Ivo, Beth, Peter<br />
<br />
== Discussion and Action Items (2008-12-19): ==<br />
<br />
* What is minimum that is absolutely necessary? mechanism to publish: create form (auto-add to registry & email & widget for human-authentication)<br />
** Action: Natasha - weekly update of bioportal with latest biositemaps<br />
** Action: Ivo - weekly update of iTools already done<br />
** Action: Beth - <strike>document the fact that HTTP will inform last date/time of biositemaps file update</strike> (done)<br />
** Action: Beth - registration form for adding biositemaps to registry<br />
** Action: Beth - Grep-like application against all biositemaps (Use Csongor's editor in browse only for presentation)<br />
** Action: Csongor - browseable mode for biositemaps editor<br />
<br />
* Do we have a good information model? Do we have good documentation?<br />
** Action: Someone (Natasha?) to email Joy at Stanford to review biositemap web site after above minimum requirements are met (e.g. here is where your current biositemap, how to view, update, etc.)<br />
<br />
* Note: Csongor back on January 8th<br />
<br />
* Note: Next meeting on 1-16-2008 (Beth to email reminder in January) <br />
<br />
== Outstanding action items: ==<br />
<br />
* Beth & Csongor: work on merging apis (complimentary functionality) upon his return from Australia (week of Dec. 15)<br />
** Csongor & I need to talk about this, but given all the editor work that is on Csongor's plate, I believe Michigan should be able to do this work <br />
<br />
* Csongor: Update Biositemaps Editor to allow invalid classes<br />
** Csongor, can this be done by end of January?<br />
<br />
* Beth & Peter: follow up with NCBC centers to publish & update biositemaps (note I2B2 & CCB use deprecated classes that need to be updated)<br />
** wait on this until other outstanding issues are completed <br />
** <strike>comment out deprecated classes for now</strike> (done)<br />
<br />
* Ivo: Update iTools application to consume new biositemaps RDF files via RDF-to-XML web service<br />
** Ivo/Natasha: Outstanding issues listed in followup email <br />
<br />
* There are problems with the database or bioportal that need to be resolved in order to expose NCBC resources on bioportal<br />
** Natasha: early January release should fix this<br />
<br />
* Beth: will clarify who will develop biositemaps search application following CTSA call regarding BRO/IM harmonizing<br />
** While we didn't get a chance to discuss this on the CTSA call, Michigan is willing to work on this with a target date early in 2009 (an exact date wouldn't be available until we can get our team to meet after the holidays).<br />
<br />
* Modify Biositemaps Editor to support multiple resource types<br />
** Csongor: to be done early next year (January 2009)<br />
<br />
* Modify Biositemaps Editor to support harmonized CTSA biositemaps information model:<br />
** Csongor: update editor<br />
** Question: Can Harpreet to write converter? <br />
<br />
* The expanded/harmonized biositemap has 25 possible properties which should be reviewed/trimmed down if possible <br />
** Byline will be dropped<br />
** Language and platform kept as optional<br />
** biositemap_author kept as optional (note that CTSA wants this not displayed in the editor -- they see it as a disincentive)<br />
<br />
* A significant outcome of the harmonizing call was the much broader definition of what is a Biomedical Resource that CTSA uses. Nancy and Harpreet were planning on following up with their proposed additions to the BRO first week of January<br />
<br />
==Biositemaps Web-Services Specifications==<br />
===I. Biomedical Resource Ontology (BRO) ontology=== <br />
* (http://bioportal.bioontology.org/virtual/1104). The following methods/functions will be valuable:<br />
** getBRO(): returns an XML with the complete current BRO hierarchy (starts with BRO root node)<br />
** getParents(BRONode): returns an XML with the meta-data of all the parents (in the BRO hierarchy), given BRONode. Most of the time there will be 1 parent, but there may be many<br />
** getChildren(BRONode): returns an XML with the meta-data of all the children (in the BRO hierarchy), given BRONode<br />
** getPartialBRO(BRONode): returns an XML with the meta-data of the BRO sub-hierarchy starting with BRONode<br />
** getSiblings(BRONode): returns an XML with the meta-data of all the siblings (in the BRO hierarchy) of the given BRONode (same hierarchy level)<br />
<br />
===II. Information Model (IM)===<br />
* http://www.ncbcs.org/biositemaps/formatDescription.html. The following methods/functions will be valuable:<br />
** getBiositemapsIM(): returns an XML with the meta-data of all the required/formal IM fields, their properties and descriptions. Like in: http://www.ncbcs.org/biositemaps/formatDescription.html<br />
** getBiositemapsIM_Property(int): returns an XML with the property-name of the IM field index by "int".<br />
** getBiositemapsIM_Description(int): returns an XML with the description of the provided IM field index by "int"<br />
** getBiositemapsIM_Description(property): returns an XML with the description of the provided IM property-name<br />
** getBiositemapsIM_Optional(property): returns an XML with the triples (name, property, value) of all non-standard, optional and non-core IM fields.<br />
<br />
===III. General Biositemaps.RDF web-service that provide not only the standard/required/IM meta-data, but any project/center/field- specific meta-data provided by the Biositemap creator/curator===<br />
: That is, we can have a center that has created a new Biositemap.RDF object, which contains the triple (name=NewField; property=NewProperty; value=NewValue). Suppose, "NewField" is *not* in the Biositemaps IM. We still need to provide services for people/ tools to retrieve this triple in XML, just like we allow retrieval of IM fields. This may be relatively easy, once we have the first two extensions (I. and II.).<br />
<br />
==[http://itools.ccb.ucla.edu/ iTools] processing (consumption/production) of Biositemaps.RDF==<br />
* Date: 01/14/09<br />
* Status of the current implementation of [http://itools.ccb.ucla.edu/ iTools] Yahoo-WebSearch of Biositemaps.RDF<br />
** [http://itools.ccb.ucla.edu/ iTools] WebSearch starts automatically every Friday morning. It may also be manually started by admins.<br />
** After the completion of the auto WebSearch, [http://itools.ccb.ucla.edu/ iTools] starts is own custom designed Web-Crawler, which traverses the entire http://www.biositemap.org/ domain and extracts all Biositemap.RDF objects there.<br />
** Finally [http://itools.ccb.ucla.edu/ iTools] combines both the Web-Search and the Web-Crawler results in the iTools SandBox. There are no identifiers indicating how was a Biositemaps.RDF object obtained (via web-search or web-crawling).<br />
* [http://itools.ccb.ucla.edu/ iTools] uses its own parser to parse Biositemap.RDF documents. There are 2 reasons for not using the [http://rest.bioontology.org/biositemap-server/parse?url=http://portal.ncibi.org/biositemap.rdf NCBO provided Biositemap.RDF web-service]:<br />
** The Biositemaps.XML genereated by this service does not provide a valid Biositemap.XML result (it's incompatible with the (legacy) Biositemaps.xml schema/format).<br />
** The RDF --> XML web-service converter only rewrites the RDF tags, so one needs yet another follow-up parser applied to the resulting XML object. Thus the iTools client uses its own parser to minimize the overhead.<br />
<br />
===Important Note===<br />
Note that in the new [http://www.ncbcs.org/biositemaps/formatDescription.html Biositemaps.RDF IM] there is no NCBC Center-name, which used to be a key tag in the old Biositemap.xml schema. This is now replaced by an [http://www.ncbcs.org/biositemaps/formatDescription.html Organization] tag. As a result of that, [http://itools.ccb.ucla.edu/ iTools] will not display NCBC-center-specific view in its tabular of graphical navigation panels.</div>Ivohttps://www.na-mic.org/w/index.php?title=SDIWG:Action_Items_20081219&diff=34865SDIWG:Action Items 200812192009-01-14T23:49:49Z<p>Ivo: added iTools progress 01/14/09</p>
<hr />
<div>Go back to top level of Resourcome working group discussion pages http://na-mic.org/Wiki/index.php/SDIWG:_NCBC_Resource_Yellow_Pages_and_Software_Ontologies<br />
<br />
Who: Natasha, Csongor, Ivo, Beth, Peter<br />
<br />
== Discussion and Action Items (2008-12-19): ==<br />
<br />
* What is minimum that is absolutely necessary? mechanism to publish: create form (auto-add to registry & email & widget for human-authentication)<br />
** Action: Natasha - weekly update of bioportal with latest biositemaps<br />
** Action: Ivo - weekly update of iTools already done<br />
** Action: Beth - <strike>document the fact that HTTP will inform last date/time of biositemaps file update</strike> (done)<br />
** Action: Beth - registration form for adding biositemaps to registry<br />
** Action: Beth - Grep-like application against all biositemaps (Use Csongor's editor in browse only for presentation)<br />
** Action: Csongor - browseable mode for biositemaps editor<br />
<br />
* Do we have a good information model? Do we have good documentation?<br />
** Action: Someone (Natasha?) to email Joy at Stanford to review biositemap web site after above minimum requirements are met (e.g. here is where your current biositemap, how to view, update, etc.)<br />
<br />
* Note: Csongor back on January 8th<br />
<br />
* Note: Next meeting on 1-16-2008 (Beth to email reminder in January) <br />
<br />
== Outstanding action items: ==<br />
<br />
* Beth & Csongor: work on merging apis (complimentary functionality) upon his return from Australia (week of Dec. 15)<br />
** Csongor & I need to talk about this, but given all the editor work that is on Csongor's plate, I believe Michigan should be able to do this work <br />
<br />
* Csongor: Update Biositemaps Editor to allow invalid classes<br />
** Csongor, can this be done by end of January?<br />
<br />
* Beth & Peter: follow up with NCBC centers to publish & update biositemaps (note I2B2 & CCB use deprecated classes that need to be updated)<br />
** wait on this until other outstanding issues are completed <br />
** <strike>comment out deprecated classes for now</strike> (done)<br />
<br />
* Ivo: Update iTools application to consume new biositemaps RDF files via RDF-to-XML web service<br />
** Ivo/Natasha: Outstanding issues listed in followup email <br />
<br />
* There are problems with the database or bioportal that need to be resolved in order to expose NCBC resources on bioportal<br />
** Natasha: early January release should fix this<br />
<br />
* Beth: will clarify who will develop biositemaps search application following CTSA call regarding BRO/IM harmonizing<br />
** While we didn't get a chance to discuss this on the CTSA call, Michigan is willing to work on this with a target date early in 2009 (an exact date wouldn't be available until we can get our team to meet after the holidays).<br />
<br />
* Modify Biositemaps Editor to support multiple resource types<br />
** Csongor: to be done early next year (January 2009)<br />
<br />
* Modify Biositemaps Editor to support harmonized CTSA biositemaps information model:<br />
** Csongor: update editor<br />
** Question: Can Harpreet to write converter? <br />
<br />
* The expanded/harmonized biositemap has 25 possible properties which should be reviewed/trimmed down if possible <br />
** Byline will be dropped<br />
** Language and platform kept as optional<br />
** biositemap_author kept as optional (note that CTSA wants this not displayed in the editor -- they see it as a disincentive)<br />
<br />
* A significant outcome of the harmonizing call was the much broader definition of what is a Biomedical Resource that CTSA uses. Nancy and Harpreet were planning on following up with their proposed additions to the BRO first week of January<br />
<br />
==Biositemaps Web-Services Specifications==<br />
===I. Biomedical Resource Ontology (BRO) ontology=== <br />
* (http://bioportal.bioontology.org/virtual/1104). The following methods/functions will be valuable:<br />
** getBRO(): returns an XML with the complete current BRO hierarchy (starts with BRO root node)<br />
** getParents(BRONode): returns an XML with the meta-data of all the parents (in the BRO hierarchy), given BRONode. Most of the time there will be 1 parent, but there may be many<br />
** getChildren(BRONode): returns an XML with the meta-data of all the children (in the BRO hierarchy), given BRONode<br />
** getPartialBRO(BRONode): returns an XML with the meta-data of the BRO sub-hierarchy starting with BRONode<br />
** getSiblings(BRONode): returns an XML with the meta-data of all the siblings (in the BRO hierarchy) of the given BRONode (same hierarchy level)<br />
<br />
===II. Information Model (IM)===<br />
* http://www.ncbcs.org/biositemaps/formatDescription.html. The following methods/functions will be valuable:<br />
** getBiositemapsIM(): returns an XML with the meta-data of all the required/formal IM fields, their properties and descriptions. Like in: http://www.ncbcs.org/biositemaps/formatDescription.html<br />
** getBiositemapsIM_Property(int): returns an XML with the property-name of the IM field index by "int".<br />
** getBiositemapsIM_Description(int): returns an XML with the description of the provided IM field index by "int"<br />
** getBiositemapsIM_Description(property): returns an XML with the description of the provided IM property-name<br />
** getBiositemapsIM_Optional(property): returns an XML with the triples (name, property, value) of all non-standard, optional and non-core IM fields.<br />
<br />
===III. General Biositemaps.RDF web-service that provide not only the standard/required/IM meta-data, but any project/center/field- specific meta-data provided by the Biositemap creator/curator===<br />
: That is, we can have a center that has created a new Biositemap.RDF object, which contains the triple (name=NewField; property=NewProperty; value=NewValue). Suppose, "NewField" is *not* in the Biositemaps IM. We still need to provide services for people/ tools to retrieve this triple in XML, just like we allow retrieval of IM fields. This may be relatively easy, once we have the first two extensions (I. and II.).<br />
<br />
==[http://itools.ccb.ucla.edu/ iTools] processing (consumption/production) of Biositemaps.RDF==<br />
* Date: 01/14/09<br />
* Status of the current implementation of [http://itools.ccb.ucla.edu/ iTools] Yahoo-WebSearch of Biositemaps.RDF<br />
** [http://itools.ccb.ucla.edu/ iTools] WebSearch starts automatically every Friday morning. It may also be manually started by admins.<br />
** After the completion of the auto WebSearch, [http://itools.ccb.ucla.edu/ iTools] starts is own custom designed Web-Crawler, which traverses the entire http://www.biositemap.org/ domain and extracts all Biositemap.RDF objects there.<br />
** Finally [http://itools.ccb.ucla.edu/ iTools] combines both the Web-Search and the Web-Crawler results in the iTools SandBox. There are no identifies indicating how was a Biositemaps.RDF object obtained (via web-search or web-crawling).<br />
* [http://itools.ccb.ucla.edu/ iTools] uses its own parser to parse Biositemap.RDF documents. There are 2 reasons not to use the [http://rest.bioontology.org/biositemap-server/parse?url=http://portal.ncibi.org/biositemap.rdf NCBO provided Biositemap.RDF web-service]:<br />
** The Biositemaps.XML genereated by this service does not provide a valid Biositemap.XML result (it's incompatible with the (legacy) Biositemaps.xml schema/format).<br />
** The RDF --> XML web-service converter only rewrites the RDF tags, so one needs yet another follow-up parser applied to the resulting XML object. Thus the iTools client uses its own parser to minimize the overhead.<br />
<br />
===Important Note===<br />
Note that in the new [http://www.ncbcs.org/biositemaps/formatDescription.html Biositemaps.RDF IM] there is no NCBC Center-name, which used to be a key tag in the old Biositemap.xml schema. This is now replaced by an [http://www.ncbcs.org/biositemaps/formatDescription.html Organization] tag. As a result of that, [http://itools.ccb.ucla.edu/ iTools] will not display NCBC-center-specific view in its tabular of graphical navigation panels.</div>Ivo