Revising the Cell Ontology
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Revising the Cell Ontology
Terrence Meehan, Christopher Mungall, Alexander Diehl
The Jackson LaboratoryLawrence Berkeley National LaboratoryUniversity at Buffalo School of Medicine and Biomedical Sciences
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Background•Cell ontology (CL) is a candidate OBO-
Foundry ontology for in vivo cell types•Generalized, species-neutral cell types•Initially developed by Jonathan Bard,
Seung Rhee, and Michael Ashburner1
•Project funded to support the Gene Ontology
1Bard et al. Genome Biology, 6:R21 (2005)
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Increasing the Utility of the CL
•Integrate CL with other ontologies• Logical definitions (cross-products, intersections)
•Supply different ontology formats (OBO,OWL)
•Enhance content
•Promote use to the biomedical research community
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Integrating- Ontologies Referenced
An improved ontological representation of dendritic cells as a paradigm for all cell types Masci AM, BMC Bioinformatics 2009, 10:70
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Melanophage
intersection_of: CL:0000864 ! tissue-resident macrophageintersection_of: has_part CHEBI:25179 ! melaninintersection_of: part_of UBERON:0002097 ! skin of body
image from www.drmihm.com
Diehl AD, et al J Biomed Inform. 2011Meehan et al, BMC Bioinformatics. 2011
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OBO Reasoner misses Inconsistencies
has_plasma_membrane_partlacks_plasma_membrane_part
develops_from
• Contradictory axioms missed by OBO Edit Reasoner
• Negation not possible in OBO Reasoners
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Short Cut relations
has_plasma_membrane_partEquivalentTo: has_part some (GO:’plasma membrane’ and has_part some ?Y)
lacks_plasma_membrane_part- has_part exactly O (GO:’plasma membrane’ and has_part some ?Y)
•Expand the logic of OBO relationships•Use features of OWL reasoners
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Build Process- CL
= cell.obo
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Enhancing Content- cell types from the FMA•Foundation Model Anatomy (FMA)1
•Ontology of human anatomical structure•Use OBOL-• Parse cell types from ontology• attempt to automatically create logical definitions• succeeded with about 200• manually added 500
1 A reference ontology for biomedical informatics: the Foundational Model of Anatomy. Rosse C, Mejino JL Jr. J Biomed Inform. 2003 Dec;36(6):478-500
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Enhancing Content- A “win-win” for both ontologies
•Based metazoan cell types on FMA’s H. sapiens cell types
•Improved the higher level structure of CL
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Enhancing Content- A “win-win” for both ontologies
FMA
CL
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Referencing the FMA
‘muscle cell’ (CL:0000187) has xref‘muscle cell’ (FMA:67328)
EquivalentToCL:0000187 part_of some NCBITaxon:9606
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Enhancing Content- Making Room
Plant ontology
Cell line ontology (CLO)
Ontology of Biomedical Investigations (OBI)
“pruned” away plant cell types
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CL collaborating with other groups in the biomedical community
•Ontology developers•International Neuroinformatics
Coordinating Facility (INCF)•ImmPort•Functional Annotation Of the Mammalian
Genomes (FANTOM5)
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CL-INCF collaboration
Use CL to harmonize representation of cell types described in different nomenclatures
Patrick Ray, Joseph Shea
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Dr. David Dougall Dr. Scheuermann GroupUT Southwestern Medical School
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CL and FANTOM5
• Mapping transcriptional start sites using single molecule sequencer (Helicos) • Finding the transcriptional regulatory networks that define every human cell type
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Summary•We have improved the content and
structure of the CL
•Integrating with other OBO ontologies
•Continue to reach out to a wider audience
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Revising the CL- Thanks!The Jackson Laboratory
• Judith Blake• David Hill
Lawrence Berkeley National Laboratory• Suzanna Lewis
Univ. at Buffalo• Barry Smith• Alan Ruttenberg• Patrick Ray• Joseph Shea
INCF• Janis Breeze• Jyl Boline
UT-Southwestern• Richard Scheuermann • David Dougall• Lindsay Cowell Duke• Anna Maria MasciOHSU• Nicole Vasilevsky
Developers of the following:• FMA• Gene Ontology• Flybase• UBERON• Cell-Line Ontology• Protein Ontology• Plant Ontology• Ontology of Biomedical
Investigations• PATO• Zebrafish Anatomy Ontology• Phenoscape
And the participants in our two workshopsThis work was supported by an NHGRI-funded, ARRA administrative supplement grant HG002273-09Z to the
parent grant, HG002273, to the Gene Ontology Consortium and by the INCF
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Support Different Ontology versionsOBO Format OWL RDF/XML
Standard
http://purl.obolibrary.org/obo/cl.obo
http://purl.obolibrary.org/obo/cl.owl
Basic http://purl.obolibrary.org/obo/cl-basic.obo
http://purl.obolibrary.org/obo/cl-basic.owl
• Standard form = CL plus MIREOTed terms from other ontologies• Basic form = CL with MIREOTed classes and references removed• All forms of ontologies are pre-reasoned