Minutes PAG 2002

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Minutes of the Inaugural Meeting of the Plant Ontology Consortium

Location and Time

Town & Country Convention Center, Terrace Room #3
9:30 - 12:00, Saturday, January 12, 2002 (beginning of Plant, Animal & Microbes X genome Conference, San Diego, California, USA)


Agenda

� Welcome, Introductions & Apologies
� Additional items for the agenda
� Formation of the Plant Ontology Consortium

  • Composition
  • Trademark
  • Web address
  • Publications
  • Networking with other research groups

� Update/outcome of the NSF proposal for funding for the POC
� Discussion & review of the �White Paper� on the proposed Plant OntologyTM Consortium
� Plans for 2002
� Other relevant matters
� Opportunity to share & review our progress on ontology and controlled vocabulary development that various of us are working on (Reports).



Welcome:
Leszek � Welcomed all the participants to this �ground breaking� meeting to identify consensus through a �round table discussion�.

participants:

� Leszek Vincent: MaizeDb/Maize Mapping Project - a plant systematist/botanist; prime mover in compilation of the �common skeleton� whitepaper.
� Klaus Mayer: MIPS, Munich � Arabidopsis Genome, now European PlaNet, long involvement in �functional categories� MIPS GO, expanding interest in plants.
� Jeff Ning: KSU, Postdoc, Biologist ? Bioinformatics; project with Jan Leach, Rice Mutants, Scot Hulbert; own project, gene prediction algorithm development.
� Ken McNally: GRC, IRRI � allele mining of IRRI germplasm collection using comparative genomics.
� Junjian Ni: Gramene (Cornell Univ.), mutant control vocabularies with Pankaj Jaiswal.
� XiaoRang Pan: CSHL, Bioinformatics postdoc, computer background, working on Gramene, database work for Arabidopsis, especially mutant database (Rob Martiensen?), Arabidopsis / maize.
� Koji Doi: National Institute of Agrobiological Sciences (NIAS), Japan � construction of rice cDNA project, applying ontology to rice cDNA.
� Kenichi Higo: National Institute for Agrobiological Sciences, Associate Director RGP, Gene sequence � Sakata; map-based cloning, rice knockout, proteome, cDNA project each project construct links; cis element database (his special project), needs to link to other databases efficiently.
� Michael Ashburner: GO representative (Drosophila), Flybase curator, Drosophila melanogaster genome 1998 consortium, former director of EBI.
� Susan McCouch: Cornell Univ., Gramene Co-PI; 8 years beforehand, RiceGenes (no controlled vocabulary), systematic approach QTL & mutant phenotypes, need to solidify traits and characteristics; trait ontology using GO.
� Pankaj Jaiswal: Cornell Univ./Gramene; trait ontology for plants (initially rice); contributing to development of controlled vocabulary - specifically for monocots; GO rice protein database (8,000 proteins so far).
� Richard Bruskiewich: International Rice Research Institute (IRRI); Bioinformatics Specialist involved in bioinformatics support of functional genomics and germplasm characterization, especially, the International Rice Information System (IRIS) for which gene, trait and (mutant) phenotype ontologies are being developed.
� Lin Huang: UK CropNet (IGER - John Innes), forage grasses mainly.


Apologies: Leonore Reiser, TAIR
Ed Coe, Mary Polacco � MaizeDB


Additional items for the agenda: No further items were tabled.

Formation of the Plant Ontology Consortium:

Short history:
- formed through networking; 2 years ago, Leszek Vincent met Leonore Reiser at the annual Maize Genetics Conference in Idaho; Leonore asked Leszek about CV/O for maize?
- GO users network
- Contact with Michael Ashburner
- Pankaj @ meeting last year proposed drafting a common skeleton doc. ( as a �white paper�, one portion of this meeting�s agenda
- 3 core participants so far:
Gramene (CSHL/Cornell; Lincoln Stein is PI)
IRRI
MaizeDB

TAIR is closely associated with the work of the POC.


Question: are any other core participants needed?

GO - Open meetings are �self funded� by participants, not GO. Very little overhead, some central funding for WWW etc needed & for central coordination; don�t want too many participants in core of POC. Other potential database participants � keeping core group small is a pragmatic not autocratic decision.

Trademark � LV contacted GO (Mike Cherry); Recommended to use unregistered trademark (TM) adjacent to �Plant Ontology� i.e. Plant OntologyTM.

Pankaj � TM needs to be traded on the commercial market before it can be registered as such; currently, only have a copyright (C with a circle). It should be enough.

KM (MIPS) - databases are copyrighted.

Trade Mark(TM) considered by some to be inappropriate, COPYRIGHT or SERVICE MARK better?

Leszek to follow-up. [Follow-up: A trademark is a name, symbol, word, or combination of 2 or more of these that a person places on goods that the person sells or distributes, a container of the goods, a display associated with the goods, or a label or tag affixed to the goods, to identify those goods that the person makes or sells, and to distinguish them from goods that another person makes or sells. Use of �TM� for Plant Ontology is in reference to the distribution of the products of the POC. Consequently Plant OntologyTM appears appropriate. Confirmed by Legal Office at UM-C.]


- Gramene already has a WWW page (www.gramene.org) with links to plant ontology info.
- The SPRIG site (Specialized Plant Resources for Informatics and Genomics) at www.bioinformatics.org/sprig/poc has some provisional info. on the POC prior to the development of the POC website.
- Gramene also has some web & data resources which will be shared.
- MaizeDB has purchased www.plantontology.org for 10 years.
- Publications � would like to publish: RMB � contacted by Jo Wixon @ John Wiley & Sons; will be seeking PAGM info. for publication in Comparative & Functional Genomics journal.
- Networking with other research groups: - word of mouth.


Update/outcome of the NSF proposal for funding for the POC
Grant proposal submitted to NSF in June 2001 (RCN program: Research Coordination Network). 21 proposals submitted in 2001, 7 accepted for funding, ours was not, but was recognized as a valuable and necessary.

Panel summary:
- POC, Excellent idea
- Need �proof of concept� data (live prototyped database with interfaces)
- Need to identify �de novo� activities; a clear action plan involving the GO consortium

Susan McCouch � need to actually start doing some PO work, get a track record of activity & credibility & then reapply to NSF for funding (by 28 June 2002). Conclusion: let�s get started on the �real� work.


Discussion & review of the �White Paper� on the proposed Plant OntologyTM Consortium
Michael Ashburner � philosophical viewpoints�
1. Major GO mistake: Spent a lot of time, but not enough, on semantics and on the precise meaning of what a �term� in GO really is. Ashburner & Lewis have written a paper on semantics of terms & relationships between terms. This topic is not addressed in initial GO papers.
2. GO terms are equivalent to concepts, not a physical substance, but a concept-subconcept, semantic relationships, 2 relationships currently used in GO (ISA, PARTOF); not used consistently from beginning of GO work.
3. Read �WordNet� article � reference, by MIT press, a lexical database, early chapter is very instructive & provides good info. on relationships (ISA & PARTOF).
4. ISA and PARTOF relationships (represented by % and < symbols respectively in syntax) are very complex: in the cellular component, usually means component of an organelle. In process, is a subprocess. Cognitive scientists distinguish half a dozen �PARTOF� relationships.
5. Need for work on mutant phenotypes:

Michael Ashburner provided the following table representing the skeleton of thoughts regarding recording descriptive info. in ontologies.

Noun
have
determined by
Attributes by assay
have Done under
Values conditions
have
Qualifiers


� GOBO (Global Open Biology Ontologies) � overall family of biological ontologies (get from MA)
Would be the following things:
Web site:
Best practice guidelines:
Open source
Share a syntax, tools � DAG, Amigo, DAML-OIL
Namespace
CVS repository
Namespace server for prefixes (XML�
Gene
Gene Attribute
Gene Structure
Variation (EBI)
Gene product
GO
Protein family (Interpro)
Chemical
i) Biochemical substance (LIGAND)
ii) Pathway (KEGG, etc)
Development {models} � GO/temporal
Anatomy {models}
i) Gross
ii) Tissue
iii) Cell-type
Phenotype
Mutant
Trait
Pathology
Disease
Experimental conditions {MGED (MIAME/MAGE-ML), MIAFG}
Taxonomy {NCBI - TAXMAN}
Cross-Product methodologies to combine ontologies, select two subgraphs, make cross product in DAG-Edit, inheritance rules?


�WHITE� PAPER - Discussion:

  • Mike A. � use database abbreviations in GO
  • Mike A. � use NCBI THXMAN for taxonomy
  • Pankaj, Susan � Use accepted botanical terms
  • Mike A. � GO cannot have �same string� but not same identifier; identifier & definition; �sensu� only used for concept with identical lexical strings but in different domains, not used to restrict the domain of application, but lexical use of the term; David Botstein argument early in GO suggested that taxonomic restrictions in GO are not required
  • Michael A., Richard B. (Pankaj) � anatomy and morphology are synonymous, a continuum.
  • Susan � languages other than (American) English?
  • - Mike � No. Multilanguage thesauri?
  • Susan �









Reports
GRAMENE report � handout provided. 3D feature space�More info at http://www.gramene.org/plant_ontology/


IRRI � embedding GO schema into IRIS; moving IRIS terms into database (with Gramene); hired an MSc. Biologist to help so more productivity.

MaizeDB:
� Worked on white paper
� Working on Maize-specific ontologies
� Discussion with TAIR: bottom-up approache � work on taxon specific needs first, then merge.
� Working with John Richter � discovering bugs with DAG tool.

MIPS: Phenotype database for Arabidopsis, 1200 described AT phenotypes, gene names


Post-meeting comment:
1. The discussion & review of the 'White Paper� on the proposed Plant OntologyTM Consortium must be considered to be largely incomplete. It may be difficult to provide an opportunity to explicitly �ratify� this document amongst POC collaborators.

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