developing anatomy ontologies in the context of others
Post on 23-Feb-2016
27 Views
Preview:
DESCRIPTION
TRANSCRIPT
Developing anatomy ontologies in the context of others
Melissa Haendel, Chris Mungall, Carlo Torniai, Matt Yoder
lung
lung
respiratory gaseous exchange
lobular organ
parenchymatous organ
solid organ
pleural sac
thoracic cavity organ
thoracic cavity
multicellular organismal process
abnormal lung morphology
abnormal respiratory system morphology
GO
MPO
MA
FMA
abnormal pulmonary acinus morphology
abnormal pulmonary alveolus morphology
lungalveolus
respiratory system process
organ system
respiratory system
Lower respiratory
tract
alveolar sac
pulmonary acinus
organ system
respiratory system
EHDAA2
lung
lung bud
respiratory primordium
pharyngeal region
develops_frompart_of
is_a (SubClassOf)
surrounded_by
The problem: Data Silos
Differences in bone and bone tissue representation
Ontology alignment
How to synchronize anatomy ontologies
“mapping”
Xref strategy imports/MIREOT
Three approaches:
There are issues with mappingsClass A Class B In Bioportal? Useful?
FMA extensor retinaculum of wrist
MA retina Yes No
FMA portion of blood MA blood No Yes
ZFA Macula MA macula Yes No
ZFA aortic arch MA arch of aorta Yes Dubious
ZFA hypophysis MA pitiuitary No Yes
FMA tibia FBbt tibia Yes No
FMA colon GAZ Colón, Panama Yes No
PATO male Chebi maleate 2(-) Yes No
Zebrafish terms are is_a subtypes of teleost terms
is_a
Zebrafish Anatomy Teleost Anatomy Ontology
Reconciliation and linking between TAO and ZFA
Logic implemented via Xrefs- difficult to keep synchronized
OBO relations between ontologies
treat-xrefs-as-equivalent: CAROtreat-xrefs-as-equivalent: GOtreat-xrefs-as-equivalent: VSAOtreat-xrefs-as-is_a: VHOGtreat-xrefs-as-reverse-genus-differentia: MA part_of NCBITaxon:10088
These are some assertions in UBERON, and relate the Xrefs in Uberon to classes in other ontologies using specificied semantics. This allows merging of ontologies in taxonomically appropriate ways
Zebrafish terms are is_a subtypes of teleost terms
is_a
Zebrafish Anatomy Teleost Anatomy Ontology
Reconciliation and linking between TAO and ZFA
Logic implemented via Xrefs- difficult to keep synchronized
X
Using Uberon for alignment facilitates identification of missing classes
Ontology alignment
anatomical structure
endoderm of forgut
lung bud
lung
respiration organ
organ
foregut
alveolus
alveolus of lung
organ part
FMA:lung
MA:lung
endoderm
GO: respiratory gaseous exchange
MA:lung alveolus
FMA: pulmonary
alveolus
is_a (taxon equivalent)
develops_frompart_of
is_a (SubClassOf)
capable_of
NCBITaxon: Mammalia
EHDAA:lung bud
only_in_taxon
pulmonary acinus
alveolar sac
lung primordium
swim bladder
respiratory primordium
NCBITaxon:Actinopterygii
Uberon classes connect to other ontologies via a variety of relations
Uberonclasses
Synchronization by import across ontologies
One can import a whole ontology or just portions of another ontologyMIREOT: Minimum information to reference an external ontology term
CARO
VSAO
Present TAO Modularized ontology
zebrafish
caro / uberon/allcell tissue
metazoa
muscletissue
vertebrata
mesonephros
limb
arthropoda
antenna
teleost
weberian ossicle
mammalia
mammary gland
nervous system
mollusca
foot
cephalopod
tentacle
mantle
drosophila
neuron types XYZ
mushroom body
brachial lobe
NO pons
vertebravertebralcolumn
circulatory system
appendage
mesoderm
gut
tibia
gland
bone
skeletaltissue
parietalbone
fin
gonad
trachea
respiratoryairway
cross-ontologylink (sample)
amphibia
tibiafibula
larva
shellcuticle
skeleton
import
mouse human
Leveraging an integrated set of ontologies
Proposed model moving forward
Maintain series of ontologies at different taxonomic levels- euk, plant, metazoan, vertebrate, mollusc, arthropod,
insect, mammal, human, drosophila Each ontology imports/MIREOTs relevant subset of
ontology “above” it- this is recursive
Subtypes are only introduced as needed Work together on commonalities at appropriate
level above your ontology
• To get the imports working well• To have distributed social responsibility assigned• Design patterns to ensure we are all doing the same thing• To check for consistency and errors across multiple ontologies using reasoners to get correct results for all users
-These ontologies are supposed to be orthogonal but aren’t always
• Visualization tools that can aid non-ontology experts in identifying errors across multiple ontologies
Modularizing ontologies – We need:
Modularizing ontologies
Identify key points of integration between ontologies Invest energy in understanding what is out there, i.e. seek to import and reuse, rather than “aligning” later
Modularize based on domain or taxon
Let the reasoner help do the work
Work together to distribute work
Idealized protocol for new AOs
1. Collect draft list of classes, build design documents
2. Subdivide into anatomical domains, taxonomic levels, and/or differentiating characteristics
3. Request new classes from existing AOs, stub in in your own ontology, make annotations to this effect (e.g. include tracker IDs)
4. Import pre-reasoned subset from other ontologies
5. Build your ontology
More about using ontologies together-post-composition
(seta and 'is bearer of' some White) and (part_of some head)RO/BFO
HAO PATO HAO
RO/BFO
Ontologies can help reconcile annotation inconsistencies
top related