SDIWG:Meeting Minutes 20080416

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Minutes of a tcon on 20080416

Subject: Tcon on the future of the Biomedical Resource Ontology (BRO) and its integration into biositemaps.

Top page of ncbcs.org web site which is maintained by the NCBCs themselves

Top page of SDIWG web site

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

Attendees

Attendees: Maryann Martone (UCSD), Bill Bug (UCSD), Ivo Dinov (UCLA), Daniel Rubin (Stanford/NCBO), Mark Musen (Stanford/NCBO), Karen Skinner (NIH/NIDA), Peter Lyster (NIH/NIGMS)

For background materials, you can read from the top of this thread starting with Agenda. If you are more familiar with the background you can immediately go to Meeting minutes below.

Agenda

Formulate a plan how to implement the Biomedical Resource Ontology (BRO) http://alpha.bioontology.org/visualize/Biomedical_Resource_Ontology. I (Peter Lyster) suggest I start off by posing a purpose statement: the Biomedical Resource Ontology (BRO) ( view original BRO Requirements document) is an enabling technology for biositemaps Biositemaps white paper v3.2 and it may also be used in any application where a classification of biomedical resources (material or electronic) is needed. Unless there is fundamental disagreement with this I suggest we move quickly to the ‘how do we develop the BRO’ part.

To prime the discussion, I include notes and some suggestions I have accumulated from discussions I have had with a number of you recently:

BRO can currently be ‘seen’ at (http://alpha.bioontology.org/visualize/Biomedical_Resource_Ontology or for a view of the overall hierarchy in one Protégé frame http://bioontology.org/projects/ontologies/SoftwareOntology/). There are a lot of elements of BRO in NIFSTD, OBI, NITRC,… So the immediate question is whether the BRO can become the ‘mother ship’ for various resource ontologies, i.e., which can build on the BRO.

Currently (I think) the high-level BRO is in need of reorganization/redesign. Indeed NIFSTD high level “Resource Types” may be a better start. Thus I suggest (with some modifications) for the top-level BRO: Data Resource; Bibliographic Resource; Software; Research Supplies; Portals; Funding Source

I think that there are two ways we could proceed in developing the BRO: (i) continue separately in bioontology.org and reconcile with NIFSTD, OBI, NITRC etc by ‘hand’ and with mappings; (ii) make BRO a ‘view’ of NIFSTD or OBI, thus there will be less ‘hand’ work but will have to reconcile structure.

Comments before the discussion: We should probably adopt the first approach (i.e., (i) above). As a suggestion: first we might reorganize/redesign BRO using input from the extant BRO as well as NIFSTD, OBI, NITRC, CTSA. We might also use principles of OBO Foundry for ontology design (http://www.obofoundry.org/crit.shtml). Names of individuals who could do this first cut, in advance of going to the NCBC reps: Bug, Martone, Dinov, Rubin, Noy, Mungall, Nyulas, Kirschner, Kennedy, Smith, Ruttenberg, Neumann, … (please add more names as appropriate?).

Meeting Minutes

The main goal of the tcon was to generate a development path for the Biomedical Resource Ontology (BRO http://alpha.bioontology.org/visualize/Biomedical_Resource_Ontology or for a view of the overall hierarchy in one Protégé frame http://bioontology.org/projects/ontologies/SoftwareOntology/), which is being produced as part of the biositemaps (http://www.ncbcs.org/biositemaps and http://na-mic.org/Wiki/index.php/SDIWG:_NCBC_Resource_Yellow_Pages_and_Software_Ontologies) initiative under the NIH Roadmap National Centers for Biomedical Computing (NCBC). During discussions most of the actionable items posed above were agreed to; these will be summarized below. During the tcon, Bill Bug mentioned the Digital Entity and Non-realizable Information Entity (DENRI) effort. According to https://wiki.cbil.upenn.edu/obiwiki/index.php/DigitalEntityTerms the DENRI is an OBI Branch concerned with identifying entities and relations to describe information entities that can be interpreted by a computer or documented and communicated. The DENRI has much of the same content (classes) and relationships (is_a and others) which are extant or planned under BRO. The main conclusion of the tcon was that the NCBC team should continue on its current path, with a possible view to harmonizing (merging?) with the OBI/DENRI-NIFSTD-NITRC development path later on. The first action item is to form a ‘tiger team’ of staff under the NCBC should reorganize/redesign the existing BRO with the following organizing principles (one of whose goals is to enable the possible future harmonize/merge with OBI/DENRI-NIFSTD-NITRC):

(i) Use the OBO Foundry Principles in order to develop ‘healthy’ ontology (extensible, maintainable, reusable, orthogonal, etc.) http://www.obofoundry.org/crit.shtml

(ii) At all stages of the development path for BRO (especially early on) try to align BRO with NIFSTD, OBI/DENRI, NITRC so that future mappings (and this is intended to be a technical term) will be as simple, efficient, consistent, and effective as possible. Proposed members of the tiger team are: Ivo Dinov and Daniel Rubin (maintain continuity with extant effort), Peter Lyster (NIH Program), Natasha Noy (deep technical knowledge, to be confirmed since she was not present at tcon).

(iii) Enable the BRO to be extensible to other relevant fields and initiatives (NIF, OBI, NITRC, and beyond) and initiatives in biocomputing. During the tcon the concept of ‘modularity’ was discussed. The following issues were briefly mentioned by Peter Lyster but not discussed at length: what principles should we use for ‘branching’? That is, a monolithic BRO is unlikely, but a well-constructed cluster of BROs may be promoted as the ‘mother ship’. Also, Peter mentioned that the biositemaps team has yet to address the issue of stratification of resources, e.g., how to advise potential users and implementers of biositemaps content as to how to stratify the representation of their resources.

Action items

(i) Tiger team reorganize/redesign BRO (start out basically by doing it on paper and then work using tcon/Access) with top-level classes: Data Resource; Bibliographic Resource; Software; Research Supplies; Portals; Funding Source. The existing classes should be reused (http://alpha.bioontology.org/visualize/Biomedical_Resource_Ontology or for a view of the overall hierarchy in one Protégé frame http://bioontology.org/projects/ontologies/SoftwareOntology/), but it is noted that some of the extant classes are actually ‘compound classes’.

(ii) Tiger team consult with (at least) Maryann Martone, David Kennedy, and Bill Bug to ensure that the BRO conforms to the above-described organizing principles. This will also need the input from interested stakeholders: David Kennedy (NITRC), Alan Ruttenberg, Barry Smith, Yves Lussier, Chris Mungall, Beth Kirschner, Karen Skinner, Zohara Cohen, Eric Neumann, SDWIG contacts from all seven NCBCs (HV Jagadish, Will Schroeder, Aris Floratos, Shawn Murphy, Jeanette Schmidt).

(iii) Reconnect with the biositemaps timeline as described in the SDIWG tcon of 20080222 http://www.na-mic.org/Wiki/index.php/SDIWG:Meeting_Minutes_20080222#Minutes