Transcript Revising_CLx - ICBO

Revising the Cell Ontology
Terrence Meehan, Christopher Mungall,
Alexander Diehl
The Jackson Laboratory
Lawrence Berkeley National Laboratory
University 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 macrophage
intersection_of: has_part CHEBI:25179 ! melanin
intersection_of: part_of UBERON:0002097 ! skin of body
Diehl AD, et al J Biomed Inform. 2011
Meehan et al, BMC Bioinformatics. 2011
image from www.drmihm.com
OBO Reasoner misses Inconsistencies
• Contradictory axioms missed by
OBO Edit Reasoner
• Negation not possible in OBO
Reasoners
develops_from
has_plasma_membrane_part
lacks_plasma_membrane_part
Short Cut relations
• Expand the logic of OBO relationships
• Use features of OWL reasoners
has_plasma_membrane_part
EquivalentTo: 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)
Build Process- CL
= cell.obo
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
Enhancing Content- A “win-win” for
both ontologies
FMA
CL
Referencing the FMA
‘muscle cell’ (CL:0000187) has xref
‘muscle cell’ (FMA:67328)
EquivalentTo
CL:0000187 part_of some NCBITaxon:9606
Enhancing Content- Making Room
Ontology of Biomedical Investigations (OBI)
Cell line ontology (CLO)
“pruned” away plant cell types
Plant ontology
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
Dr. David Dougall
Dr. Scheuermann Group
UT Southwestern Medical School
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 Masci
OHSU
• 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/c
l.owl
Basic
http://purl.obolibrary.org/obo/
cl-basic.obo
http://purl.obolibrary.org/obo/c
l-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