The HCLS Community Profile: Describing Datasets, Versions, and Distributions Alasdair J G Gray Heriot-Watt University www.macs.hw.ac.uk/~ajg33 [email protected]@gray_alasdair Michel Dumontier Stanford University M. Scott Marshall MAASTRO Clinic 30/11/2016 @gray_alasdair www.macs.hw.ac.uk/~ajg33 1
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The HCLS Community Profile: Describing Datasets, Versions, and Distributions
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@gray_alasdair www.macs.hw.ac.uk/~ajg33
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The HCLS Community Profile: Describing Datasets, Versions, and Distributions
Alasdair J G GrayHeriot-Watt University www.macs.hw.ac.uk/[email protected]@gray_alasdair
Michel DumontierStanford University
M. Scott MarshallMAASTRO Clinic
30/11/2016
Open PHACTS Example
Data Cache (Triple Store)
Semantic Workflow Engine
Linked Data API (RDF/XML, TTL, JSON) DomainSpecificServices
Identity Resolution
Service
IdentifierManagement
Service
“Adenosine receptor 2a”
EC2.43.4CS4532
P12374
Cor
e Pl
atfo
rm
ChEMBL-RDF
ChEMBLv13
Chem2Bio2RDF
SD
v13v12
v2 or v8
Which ChEMBL version?
@gray_alasdair www.macs.hw.ac.uk/~ajg33 3
Open PHACTS Example
OPS Example
Data Cache (Triple Store)
Semantic Workflow Engine
Linked Data API (RDF/XML, TTL, JSON) DomainSpecificServices
Identity Resolution
Service
IdentifierManagement
Service
“Adenosine receptor 2a”
EC2.43.4CS4532
P12374
Cor
e Pl
atfo
rm
ChEMBL-RDF
ChEMBLv13
Chem2Bio2RDF
SD
v13v12
v2 or v8
Open PHACTSDiscovery PlatformHistoric Use Case
~January 2012
Open PHACTS v2.1ChEMBL 20
http://tiny.cc/ops-datasets
Which ChEMBL version?
@gray_alasdair www.macs.hw.ac.uk/~ajg33 6
Challenges• Datasets available
– In many versions over time– In different formats– From many mirrors/registries
• Datasets build on each other• Files do not carry metadata• Registries
– Can be out-of-date– Can contain conflicting information
https://www.w3.org/TR/hcls-dataset/Dumontier M, Gray AJG, Marshall MS, et al. (2016) The health care and life sciences community profile for dataset descriptions. PeerJ 4:e2331 https://doi.org/10.7717/peerj.2331