Supporting Ontology-Based Standardization of Biomedical Metadata in the CEDAR Workbench (ICBO 2017 Conference)

Supporting Ontology-Based
Standardization of Biomedical Metadata in
the CEDAR Workbench
Marcos Martínez-Romero
Stanford University
Stanford Universitymetadatacenter.org
EDAR
OR EXPANDED DATA
ION AND RETRIEVAL
CEDAR
CENTER FOR EXPANDED DATA
ANNOTATION AND RETRIEVAL
CEDAR
DAR
DAR
9/14/2017

age
Age
AGE
`Age
age (after birth)
age (in years)
age (y)
age (year)
age (years)
Age (years)
Age (Years)
age (yr)
age (yr-old)
age (yrs)
Age (yrs)
age [y]
age [year]
age [years]
age in years
age of patient
Age of patient
age of subjects
age(years)
Age(years)
Age(yrs.)
Age, year
age, years
age, yrs
age.year
age_years
Metadata are not standardized
3

age
Age
AGE
`Age
age (after birth)
age (in years)
age (y)
age (year)
age (years)
Age (years)
Age (Years)
age (yr)
age (yr-old)
age (yrs)
Age (yrs)
age [y]
age [year]
age [years]
age in years
age of patient
Age of patient
age of subjects
age(years)
Age(years)
Age(yrs.)
Age, year
age, years
age, yrs
age.year
age_years
Age-Years (NCIT)
(http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C37908)
“The length of a person's life, stated in years since birth.”
4

It’s extremely hard to:
–find experimental datasets
–understand how the experiments were
performed
–replicate study findings
5

Generating standard metadata is hard
• Submission formats rarely support
ontology terms
• No easy way of finding terms from
ontologies and including them into
metadata submissions
6

Semantic ecosystem to enable the
creation of high-quality metadata in
biomedicine
8

The CEDAR Workbench
Template Designer Metadata Editor
Template authors Metadata authors
design
templates
Metadata Repository
template
ﬁll in templates
with metadata
metadata
Public Databases
LINCS
submit
metadata
Biomedical Ontologies 9

design
templates
Metadata Repository
template
ﬁll in templates
with metadata
metadata
Public Databases
LINCS
submit
metadata
Biomedical Ontologies
The CEDAR Workbench
10

design
templates
Metadata Repository
template
ﬁll in templates
with metadata
metadata
Public Databases
LINCS
submit
metadata
Biomedical Ontologies
The CEDAR Workbench
22

{
"@context": {
"rdfs": "http://www.w3.org/2000/01/rdf-schema#",
"xsd": "http://www.w3.org/2001/XMLSchema#",
"pav": "http://purl.org/pav/",
//...
"Title": "http://purl.obolibrary.org/obo/NGS_0000055",
"Disorder": "http://purl.org/net/OCRe/OCRe.owl#OCRE900086",
"Institution": "http://semantic-dicom.org/dcm#InstitutionName",
"Principal Investigator": "http://purl.org/net/OCRe/OCRe.owl#OCRE901006",
"Study Type": "http://purl.obolibrary.org/obo/NGS_0000056"
},
"@type": "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C63536",
"Title": {
"@value": "A sample study"
},
"Disorder": {
"@id": "http://purl.obolibrary.org/obo/DOID_8986",
"rdfs:label": "narcolepsy"
},
"Institution": {
"@value": "Stanford University"
},
"Principal Investigator": {
"@value": "John Doe"
},
"Study Type": {
"@id": "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C15273",
"rdfs:label": "Longitudinal Study"
},
// ...
"schema:isBasedOn": "https://repo.metadatacenter.orgx/templates/6381a0ce-3904-4885-bc44-5caacb4ad0e6",
"schema:name": "Study metadata",
"schema:description": "Study template",
"pav:createdOn": "2017-09-05T09:50:28-0700",
"pav:createdBy": "https://metadatacenter.org/users/8d787b98-33dd-4aff-a88c-440caf452c61",
"pav:lastUpdatedOn": "2017-09-05T09:50:28-0700",
"oslc:modifiedBy": "https://metadatacenter.org/users/8d787b98-33dd-4aff-a88c-440caf452c61",
"@id": "https://repo.metadatacenter.orgx/template-instances/ffe856e7-d920-480d-a666-009041f609e3"
}
25

Value Set Creation
• Lists of permissible
values for fields
• Example:
Longitudinal study types
– Prospective study
– Retrospective study
– Hybrid design
26

Class Creation
• Dynamically define a
new class and
immediately use it
• Optionally link it to
existing classes
– Ontology maintainers
may use this
information to enrich
their ontologies
• Example:
adductor dorsalis
27

Class Creation
CEDAR Provisional Classes
(CEDARPC)
UBERON
adductor
dorsalis
adductor
muscle
subclassOf
28

Evaluation
• The LINCS Consortium
– Cellular signatures
• ImmPort
– Immunology
• AIRR Community
– Datasets acquired using sequencing
– Submission to NCBI BioSample
• Stanford University Libraries
29

Summary
• Authoring metadata is hard and time-consuming
• Authoring semantic metadata is even harder
– Lack of convenient tools for linking metadata to
ontologies in a metadata authoring workflow
• The CEDAR Workbench facilitates metadata
creation in a semantically rigorous way
– Add type and property assertions
– Constrain the values of fields to ontology terms
– Create classes and value sets
http://metadatacenter.org
http://cedar.metadatacenter.net
30

CEDAR
CEDAR
CEDAR
CEDAR
CEDAR
I
Metadata
Thanks!
31

Supporting Ontology-Based Standardization of Biomedical Metadata in the CEDAR Workbench (ICBO 2017 Conference)

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