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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
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)
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
Integrating- Ontologies Referenced
An improved ontological representation of dendritic cells as a paradigm for all cell types Masci AM, BMC Bioinformatics 2009, 10:70
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
OBO Reasoner misses Inconsistencies
has_plasma_membrane_part
lacks_plasma_membrane_part
develops_from
• Contradictory axioms missed by OBO Edit Reasoner
• Negation not possible in OBO Reasoners
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
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
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
Referencing the FMA
‘muscle cell’ (CL:0000187) has xref‘muscle cell’ (FMA:67328)
EquivalentToCL:0000187 part_of some NCBITaxon:9606
Enhancing Content- Making Room
Plant ontology
Cell line ontology (CLO)
Ontology of Biomedical Investigations (OBI)
“pruned” away plant cell types
CL collaborating with other groups in the biomedical community
•Ontology developers•International Neuroinformatics
Coordinating Facility (INCF)•ImmPort•Functional Annotation Of the Mammalian
Genomes (FANTOM5)
CL-INCF collaboration
Use CL to harmonize representation of cell types described in different nomenclatures
Patrick Ray, Joseph Shea
CL and FANTOM5
• Mapping transcriptional start sites using single molecule sequencer (Helicos) • Finding the transcriptional regulatory networks that define every human cell type
Summary•We have improved the content and
structure of the CL
•Integrating with other OBO ontologies
•Continue to reach out to a wider audience
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 workshops
This 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
Support Different Ontology versions
OBO 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