XP:Meetings

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2007/07/26 : GO-CL XPs, next steps

webex/tcon

Agenda:

Review of progress

Where we left off last time:

HTML summary:

Issues to be addressed:

  • poorly defined relations: has_central_participant
  • ad hoc genus terms: assembly, germination, clustering. We don't want these cluttering GO
  • sensu terms (now less of a problem)
  • poor quality of initial Obol run


UPDATE:

go_xp_cell is obsolete; use bp_xp_cell. E.g.

Obol update

Obol is much improved, latest results for GO-CL here:

Also: brief review of how GO-CL xps fit in with other xps.

This run makes use of an extended set of relations, along the lines proposed by Bada et al, reduced to a core set. Provisional defs for the relations can be found by mousing over the relations in the html summary:

The relations are still provisional.

Note that these relations better allow us to capture the difference between complete development and developmental processes (parts of complete development)

Brief discussion on how Obol works, here is the direct obol results:

Note that obol can generate synonyms and textual definitions from the xp-defs.

Missing links in GO found by Obol using xp-defs (should be identical to the set found by the OE reasoner):

OboEdit Demo

Demo of new oboedit2.0beta features

GOC members may wish to:

 cd go
 cvs update -d
 ls obol_results

Those not in GOC, this can be browsed online:

Note the "imports" files.

These import files have relative links - they assume the obol_results directory is on your hard disk.

An even simpler way is to look at the imports file with absolute links:

this pulls in everything from the web, not your disk

Demo of the following OE features:

  • intersections editor
  • reasoner results in ontology editor panel (example: oenocyte differentiation)

Next steps

  • "promoting" latest results
  • using the reasoner as part of the curation process - at least to complete missing links

Action items arising from meeting:

  • TODO: John will add GUI dialog for approving reasoner results. This will list all implied links with a checkbox next to them:
 oenocyte differentiaion is_a epithetal cell differentiation YES/NO
 (clicking YES will remove the redundant is_a link to cell differentiation)
 microglia cell activation is_a macrophage activation ....
 
  • TODO: Ontology development groups from GO and CL will evaluate latest obol results and OE-inferred is_a links

2007/05/03 : GO-ChEBI XPs

Introduction to cross products for ChEBI folks: Using ChEBI terms to define GO process terms. Summarises work done so far by Mike Bada

Ongoing issues:

  • plurals in ChEBI
  • is_a overloading

2006/08/25 : GO-CL review

Received curated feedback from 3rd round. I have now merged the obo files from each round into a single file, made some further edits and pruned a lot of unneccessary anonymous classes

Outstanding Issues

Relations

We previously used has_participant (currently in RO). this is not sufficiently specific for our purposes.

For example, if we define cardioblast cell fate specification as: a cell fate specification which has_participant cardioblast, our definition is not sufficiently strict to exclude specification processes in which a cardioblast is participating at the beginning, and is actually fated to become something else.

There was some discussion on the obo-relations mail list, see: http://www.bioontology.org/wiki/index.php/RO:Main_Page

The core relations that have now been introduced are:

  • has_central_participant
  • has_specific_outcome
  • acts_on_population

definition: ...

Anonymous classes

An anonymous class is a class without a stable OBO identifier that is created in order to define some other term

Anonymous classes introduce an extra piece of complexity which we would rather avoid. There are 3 sources of anonymous classes in the current logical definitions:

  • Terms that need to be added to CL
  • Composite terms that may never be added to CL
  • High-level process terms

The first category is simple - we can generate a report of all new CL terms we need. An example is immune cell required for definition immune cell activation. For some we'll find CL already contains a suitable term - it's just a matter of finding the CL ID and changing the intersection_of lines. (Changing the names/synonyms to be in sync between GO and CL is optional)

The second category is harder. See http://geneontology.cvs.sourceforge.net/geneontology/go-dev/obol/go-ext/anon-xps.obo?view=log for a list. As an example, we need to define "sperm aster formation" which requies "sperm aster", which if it were to be an existing term, it would be found in the GO cellular component ontology. Adding such terms may explode GO too much (see further on in this document). The current solution is to create an anonymous term "sperm aster" defined as "an aster that is part_of a sperm" (we essentially have a nested defined term).

For many of these, we could flatten the definition to: a formation which has_specific_outcome aster and located_in sperm.

The third category refers to cases like "sperm individualization", where the definition requires a generic high level genus like "individualization" that would only be used for defining a single term. We would end up with a lot of inapproprtiate terms in GO.

For these it may be possible to rewrite the logical definitions [TODO]

Other issues

TODO: summary

OBO Files

All the logical definitions and additional anonymous classes have been collected into a single file, go_xp_cell.obo.


This obo file and supporting files are all in the geneontology.sf.net cvs project in the directory

 cvs/go-dev/obol/go-ext

The files can be downloaded via a browser here:

http://geneontology.cvs.sourceforge.net/geneontology/go-dev/obol/go-ext/

If you want to access the files via cvs (recommended), follow the instructions here:

http://sourceforge.net/cvs/?group_id=36855

Viewing the logical definitions

The logical definitions can be viewed in OBO Edit. You will need to load multiple ontologies at once, see below

Loading and viewing in OBO-Edit

To load any of these in OBO edit, you will need to load:

go_xp_cell.obo -- http://geneontology.cvs.sourceforge.net/geneontology/go-dev/obol/go-ext/go_xp_cell.obo?view=log
extra_relations.obo -- http://geneontology.cvs.sourceforge.net/geneontology/go-dev/obol/go-ext/extra_relations?view=log
cell.obo -- http://obo.sourceforge.net/cgi-bin/detail.cgi?cell
relationship.obo -- RO -- http://obo.sourceforge.net/relationship/relationship.obo
gene_ontology.obo

You will have to use the 'advanced' option in the oboedit load menu. You may have to check 'allow dangling references'

This is a lot of files to load! It has the advantage of keeping everything modular. If you don't want all the bother, the above ontologies have been combined for your convenience, at:

http://geneontology.cvs.sourceforge.net/geneontology/go-dev/obol/go-ext/ego_full.obo?view=log

The extra_relations.obo file contain some candidates for inclusion in the obo relations ontology; this list is not stable and will most likely be whittled down to a smaller set, then definitions provided. The final set of extra relations will most likely include a minimal set of extensions to has_participant, see the discussion above.