Ontology Development Progress Report December 2013

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Ontology Development Progress Report

GOC Meeting Dec 2013

Prepared and Submitted by Jane Lomax and David Hill

Personnel

  • David Hill (MGI)
  • Tanya Berardini (TAIR)
  • Heiko Dietze (LBL)
  • Harold Drabkin (MGI)
  • Becky Foulger (EBI)
  • Jane Lomax (EBI)
  • Chris Mungall (LBL)
  • David Osumi-Sutherland (EBI) (started Sept 2013)
  • Paola Roncaglia (EBI)

Ontology Editing

SourceForge Requests

SF items opened (SF items closed)

Mar 2013 [data lost in tracker transition]
Apr 2013 26 (21)
May 2013 26 (21)
Jun 2013 41 (37)
Jul 2013 46 (39)
Aug 2013 65 (55)
Sept 2013 60 (46)
Oct 2013 83 (61)
Nov 2013 65 (33)
Dec 2013 6 (0)
Total 2013 418 (313)

Term Statistics

Total number of GO terms added Jan 2013 to Dec 2013: 1365
 Total number of GO terms added manually Jan 2013 to Dec 2013:               344
 Total number of GO terms added via TermGenie template Jan 2013 to Dec 2013: 803
 Total number of GO terms added via TermGenie freeform Jan 2013 to Dec 2013: 218
Total number of GO terms obsoleted Jan 2013 to Dec 2013: 67


Major Projects

Transition to OWL

We have now completed a shift in which all ontology reasoning is performed using OWL-based reasoners run during automated jobs or manually
by ontology editors. Ontology editors were trained on the use of the Protege editor during several focus group meetings to prepare for the
OBO-OWL shift. Most ontology editing on a day-to-day basis is still performed using obo-edit and the ontologies are committed in obo
format. Once a commit is requested the GO is automatically transferred to an OWL format and the main obo file, auxiliary cross-product
files and external ontologies are checked for logical errors in the Jenkins environment. If errors are found, an automated e-mail is sent
to ontology editors indicating that the ontology build has failed the checks and a report is included that indicates where the problem was
encountered. Ontology editors can then fix the problem before the 'public' version of the ontology is released. In addition, ontology
editors use the OWL version directly in the Protege editor to test new ideas and to further troubleshoot build failures.
As a result of this work, many of the relationships in the ontology are now automatically inferred rather than manually asserted by
ontology editors. A report report listing added and deleted relationships is delivered each week to the ontology editing group as a
'sanity' check.  

TermGenie templates

Since March 2013 we have added 14 new templates to our template-based term addition tool, TermGenie. These are:

chemical_transport_from_to (CHEBI)
plant_development (PO)
plant_formation (PO)
plant_maturation (PO)
plant_morphogenesis (PO)
plant_structural_organozation (PO)
cell_apoptosis (CL)
chemical_homeostasis (CHEBI)
protein_localization_to (GO BP)
chemical_import_into (CHEBI)
cc_assembly_diassembly (GO BP & CC)
protein_complex_by_activity (GO BP & CC)
single-multiple-organism_process (GO BP)
cell_differentiation (CL)

These templates utilise both classes within GO and classes from external ontologies, shown in parentheses. PO = plant ontology, CL = cell ontology, CHEBI = chemicals of biological interest ontology.

Mappings to other ontologies

To take further advantage of the reasoning capabilities of OWL and to integrate the expertise of distributed resources, we have continued to work with developers from other groups to cross-reference GO terms with external ontologies.

Mapping Chemicals in GO to ChEBI
We have completed the first phase of our integration with The Chemicals of Biological Interest (ChEBI) resource. All terms that follow
standard patterns and are differentiated by chemical structure are defined using references to the ChEBI resource. GO ontology editors
work together with ChEBI editors to address queries about ontology alignment and to make additions to ChEBI when necessary. This work is
fully described in PMID:23895341
Mapping Reactions in GO to Rhea
This year we have embarked on a process to align GO catalytic reactions with the Rhea database of enzymatic reactions (http://www.ebi.ac.uk/rhea/). 
This project has the ultimate aim of automatically deriving most GO catalytic reactions from Rhea,    eliminating the need to curate this data in both Rhea and GO. 
This year we have worked on the cross-references to Rhea which are maintained in GO e.g. removing 1:many mappings and resolved some of the discrepancies 
between the two systems. We have also developed a pattern for the logical definitions of GO catalytic reactions in terms of the entities from the CHEBI ontology 
that participate in them.
Mapping cellular Components in GO to SAO

This year we completed the incorporation of the Neuroscience Information Framework's (NIF) Subcellular Anatomy Ontology (SAO) into GO cellular component. Our paper describing this project was published in Oct (PMID:24093723).

Improved Biological Representation

Signaling

We are constructing a signaling curation manual to provide annotation guidelines for the signaling terms. We have had a number of calls to discuss further improvements to the existing signaling structure, particularly how to define and place the intracellular signaling modules. We are standardizing and clearing up the existing signaling pathway terms, such as interferon signaling. Signaling pathways have been used as examples for the LEGO model of annotation.

Apoptosis

In 2013, the Apoptosis GO working group provided curators with detailed annotation guidance, in the shape of an apoptosis curation manual enriched with annotation examples (http://wiki.geneontology.org/index.php/Apoptosis_Curation_Manual). This guidance supported a significant curation effort that focused mostly on human and mouse apoptosis players and regulators. Feedback from curators was channeled into further polishing and adding to the apoptosis branch of the ontology. Ontology work was also done on cell death modalities other than apoptosis, with a focus on necroptosis as this was identified as a growing field of research. This effort included annotation of necroptosis players from recent literature. As a result of all the above, in 2013 over 5,000 manual annotations were added or revised in the branch under GO:0008219 'cell death'.

Viral work

We are now reaching the end of the ontology changes for the viral processes and cellular components in GO. This work has affected 334 biological process terms and 67 cellular component terms. We are drafting a paper to be submitted to BMC Microbiology.

Metabolic Pathways (Glycolysis)
We have begun work on better modeling metabolic pathways by choosing a universal pathway that although straightforward still presents
challenges for GO representation, glycolysis. Taking advantage of the knowledge in the Reactome resource, we have been working with an
expert from reactome to represent the pathway in the GO framework. As a test-case for the representation of other metabolic pathways in
GO, we have begun creating has_part links between the biological process and the molecular functions that are always a part of a process.
We are exploring the use of these representations to create individual views that can be used in a modular annotation framework.