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Datasets with bioschemas
The document discusses the development of the DATS (Data Tag Suite) model for describing scientific datasets to enable data discovery. Key points: - DATS is designed around the core entity of a "dataset" and aims to converge metadata elements from use cases and existing schemas/models in a top-down and bottom-up approach. - The DATS model and a biomedical extension have been developed through a community-driven process and are available on GitHub. - Efforts are underway to map DATS to schema.org and integrate it within initiatives like DataMed to facilitate indexing of datasets. - Learning from the DATS experience, the next steps involve developing a Bioschemas specification focused specifically
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Datasets with bioschemas
- 1. DatasetswithBioschemas Alejandra Gonzalez-Beltran(*), PhilippeRocca-Serra(*), Susanna Sansone(*) and the bioCADDIE Team and Commmunity (*) Oxford e-Research Centre, University of Oxford Bioschemas community meeting, Harpenden,Hertfordshire, UK 8th-9th November 2016
- 2. Theproblem how to describescientific(*) datasets to enable data discovery (*) considering in particular biological and biomedical datasets
- 3. Designprinciples The model fordata description to be designed around the Dataset entity, i.e. a unit of information stored by a data repository: ● Archived experimental datasets which do not change after deposition to the repository; e.g. dbGAP, GEO, ClinicalTrials.org ● Datasets in reference knowledge bases, describing dynamic concepts, such as “genes” whose definition morphs over time; e.g. UniProt Additionally: ● A dataset and related datasets may available in multiple repositories ● A dataset may be available in multiple forms
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- 5. Theapproach:convergenceofmetadataelementsderivedfromuse cases(top-down)andmodels/schemas(bottom-up) top-down approach bottom-upapproach (v1.0, v1.1, v2.0, v2.1) Modelserialisedas JSON-schemas/JSON-LD withschema.organnotations Evaluationthrough Mapping50+repositories Availablethrough DataCiteAPI, mappedtoDatacitationmetadata
- 6. Extractingrequirementsfromusecases ❖ Selected competencyquestions ✧ representative set collected from: use cases workshop, white paper, submitted by the community and from NIH and Phil Bourne’s ADDS office ✧ key metadata elements processed: abstracted, color-coded and terms binned binned as Material, Process, Information, Properties; relation identified
- 7. Mappingexistingmetadataschemas/models ❖ schema.org ❖ DataCite ❖RIF-CS ❖ W3C HCLS dataset descriptions (mapping of many models including DCAT, PROV, VOID, Dublin Core) ❖ Project Open Metadata (used by HealthData.gov is being added in this new iteration) ❖ ISA ❖ BioProject ❖ BioSample ❖ MiNIML ❖ PRIDE-ml ❖ MAGE-tab ❖ GA4GH metadata schema ❖ SRA xml ❖ CDISC SDM / element of BRIDGE model bottom-up approach https://biosharing.org/collection/bioCADDIE https://github.com/biocaddie/WG3-MetadataSpecifications/
- 8. DATS:DAtaTagSuite Coreentities Biomedicalextension Like the JATS(Journal Article Tag Suite) is used by PubMed to index literature, a DATS (DatA Tag Suite) is needed for a scalable way to index data sources in the DataMed prototype https://github.com/biocaddie/WG3-MetadataSpecifications/
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- 14. Mappingdatstoschema.org ✧ Missing elements(needed by DATS) submitted to the tracker; Roughly 80 % of DATS entities and properties can be mapped but alignment is not perfect/less precise), the remaining 20% constitute major gaps ✧ ✧ Tracking schema.org and its related Health and Life Science extension evolution (the latter focuses on clinical studies)
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- 20. Datsexportedby https://github.com/datacite/spinone/issues/3 ● An APIendpoint that returns DataCite metadata in DATS format is work in progress: http://api.datacite.org/dats ● DataCite Metadata Schema allows for a RelatedIdentifier with the HasMetadata relation type this allows linking to the DATS metadata from a DataCite metadata record Martin Fenner DataCite
- 21. DatsandDCIPsupplementmapping Citation metadata forrepositories’ landing page
- 22. Mappingbetweenomics-diandDATS ❖ Overlap withDATS core elements ✧ In red some DATS extended elements
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