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Oct 2, 2013 (3 years and 6 months ago)

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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 Ashburner
1


Project funded to support the Gene Ontology

1
Bard 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

image from
www.drmihm.com

Diehl AD,
et al
J Biomed Inform
.
2011

Meehan
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_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)




Expand the logic of OBO relationships


Use features of OWL
reasoners






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

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

Dr. David
Dougall


Dr.
Scheuermann

Group

UT Southwestern Medical School




CL and FANTOM
5



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