In this talk I describe the main features CEDAR developed to make it possible to easily construct Web-based metadata-acquisition forms, enrich those forms with ontology concepts, and then fill out the forms to create ontology-annotated descriptions of scientific experiments

1. 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
CENTER FOR EXPANDED DATA
9/14/2017

2. 2

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
Metadata are not standardized
3

4. 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
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

5. It’s extremely hard to:
–find experimental datasets
–understand how the experiments were
performed
–replicate study findings
Metadata are not standardized
5

6. 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

7. 7

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

9. 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

10. 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
The CEDAR Workbench
10

11. 11

12. 12

13. 13

14. 14

15. 15

16. 16

17. 17

18. 18

19. 19

20. 20

21. 21

22. 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
The CEDAR Workbench
22

23. 23

24. 24

25. {
"@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

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

27. 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

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

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

30. 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

31. CEDAR
CENTER FOR EXPANDED DATA
ANNOTATION AND RETRIEVAL
CEDAR
CENTER FOR EXPANDED DATA
ANNOTATION AND RETRIEVAL
CEDAR
CEDAR
CEDAR
I
Metadata
Thanks!
31