https://biocaddie.org/

1. Supported by the NIH grant 1U24 AI117966-01 to UCSD
PI , Co-Investigators at:
The model
annotated with schema.org
Susanna-Assunta Sansone, Alejandra Gonzalez-Beltran, Philippe Rocca-Serra
Oxford e-Research Centre, University of Oxford, UK

2. The model

3. What is ?
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

4. Where do I find the documentation?
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

5. A community-driven effort

6. A community-driven effort

7. v Support intended capability of the DataMed prototype to harvest
key metadata (experimental and data) descriptors, such as
² information and relations between authors, datasets, publication and
funding sources, nature of biological signal, nature of perturbation
etc.
What is support to cover and do?

8. v Support intended capability of the DataMed prototype to harvest
key metadata (experimental and data) descriptors, such as
² information and relations between authors, datasets, publication and
funding sources, nature of biological signal, nature of perturbation
etc.
v Use cases and the competency questions used throughout the
development process
² to define the appropriate boundaries and level of granularity: which
queries will be answered in full, which only partially, and which are
out of scope
What is support to cover and do?

9. Metadata elements identified by combining the two complementary approaches
top-down approach bottom-up approach
The development process in a nutshell
Model serialized as JSON schemas and mapping to schema.org
(v1.0, v1.1, v2.0, v2.1)

10. Extracting requirements from use cases
v Selected competency questions
² representative set collected from: use cases workshop, white paper, submitted by
the community and from NIH and Phil Bourne’s ADDS office
² key metadata elements processed: abstracted, color-coded and terms binned
binned as Material, Process, Information, Properties; relation identified
top-down approach

11. bottom-up approach
Mapping existing metadata schemas
v schema.org
v DataCite
v RIF-CS
v W3C HCLS dataset descriptions (mapping of many models including DCAT, PROV, VOID, Dublin
Core)
v Project Open Metadata (used by HealthData.gov is being added in this new iteration)
v ISA
v BioProject
v BioSample
v MiNIML
v PRIDE-ml
v MAGE-tab
v GA4GH metadata schema
v SRA xml
v CDISC SDM / element of BRIDGE model

12. v Metadata is either too much or too little
² many databases won’t have all these metadata elements
² conversely, domain-specific databases (e.g. focusing on a type of
study, organism or technology) have more detailed metadata
We know that one size does not fit all

13. v Metadata is either too much or too little
² many databases won’t have all these metadata elements
² conversely, domain-specific databases (e.g. focusing on a type of
study, organism or technology) have more detailed metadata
v Our goal is NOT to develop the perfect model
² we have had several iterations testing the model
² we have aimed to have maximum coverage of use cases with
minimal number of data elements
² we do foresee that not all questions can be answered in full
We know that one size does not fit all

14. v The descriptors for each metadata element (Entity), include
² Property (describing the Entity), Definition (of each Entity and Property),
Value(s) (allowed for each Property)
Key features of

15. v The descriptors for each metadata element (Entity), include
² Property (describing the Entity), Definition (of each Entity and Property),
Value(s) (allowed for each Property)
v We have defined a set of core and extended entities
² Core elements are generic and applicable to any type of datasets, like the
JATS can describe any type of publication.
² Extended elements includes an additional elements, some of which are
specific for life, environmental and biomedical science domains
² this set can be further extended as needed
Key features of

16. v The descriptors for each metadata element (Entity), include
² Property (describing the Entity), Definition (of each Entity and Property),
Value(s) (allowed for each Property)
v We have defined a set of core and extended entities
² Core elements are generic and applicable to any type of datasets, like the
JATS can describe any type of publication.
² Extended elements includes an additional elements, some of which are
specific for life, environmental and biomedical science domains
² this set can be further extended as needed
v Entities are not mandatory, in both core and extended set
² An entity is used only when applicable to the dataset to be described
² in that case only few of its properties are defined as mandatory
Key features of

17. v Model is designed around the Dataset, an entity that intends to cater for
any unit of information stored by repositories:
² archived experimental datasets, which do not change after deposition to the
repository => examples available for dbGAP, GEO, ClinicalTrials.org
² datasets in reference knowledge bases, describing dynamic concepts, such
as “genes”, whose definition morphs over time => examples available for
UniProt
v The Dataset entity is also linked to other digital research objects part of the NIH
Commons, such as Software and Data Standard, which are the focus on other
discovery indexes and therefore are not described in detail in this model
General design of the

18. v Model is designed around the Dataset, an entity that intends to cater for
any unit of information stored by repositories:
² archived experimental datasets, which do not change after deposition to the
repository => examples available for dbGAP, GEO, ClinicalTrials.org
² datasets in reference knowledge bases, describing dynamic concepts, such
as “genes”, whose definition morphs over time => examples available for
UniProt
General design of the

19. core and extended elements

20. 18 core elements

21. 18 core elements and few
mandatory properties

22. v What is the dataset about?
² Material
v How was the dataset produced ? Which information does it hold?
² Dataset / Data Type with its Information, Method, Platform,
Instrument
v Where can a dataset be found?
² Dataset, Distribution, Access objects (links to License)
v When was the datasets produced, released etc.?
² Dates to specify the nature of an event {create, modify, start, end...}
and its timestamp
v Who did the work, funded the research, hosts the resources etc.?
² Person, Organization and their roles, Grant
Core elements provide the basic info

23. Standards

24. Standards

25. Standards

26. Software

27. Software

28. Dataset distribution and access

29. also follows the W3C Data on
the Web Best Practices
DATS follows these, which
also recommend
DatasetDistribution
https://www.w3.org/TR/dwbp

30. Serializations
v DATS model in JSON schema, serialized as:
² JSON* format, and
² JSON-LD** with vocabulary from schema.org
v …serializations in other formats can also be done, as / if needed
* JavaScript Object Notation
** JavaScript Object Notation for Linked Data
Context (mapping) file also
available, meaning that other
vocabularies can be used
Discussion also ongoing with:

31. Schema.org value-added to
v Why using schema.org to annotate the DATS?
² Developed/used by search engine consortium (google, yandex, yahoo etc.)
² The NIH Commons is discussing its use
v What benefits do DataMed get by implementing a schema.org-based
DATS? Especially:
² increased visibility (by both popular search engines and DataMed), accessibility (via
common query interfaces) and possibly improve ranking

32. Schema.org value-added to
v Why using schema.org to annotate the DATS?
² Developed/used by search engine consortium (google, yandex, yahoo etc.)
² The NIH Commons is discussing its use
v What benefits do DataMed get by implementing a schema.org-based
DATS? Especially:
² increased visibility (by both popular search engines and DataMed), accessibility (via
common query interfaces) and possibly improve ranking
v Discussion and collaboration with schema.org is ongoing
² 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
² schema.org and its related Health and Life Science extension evolve (the latter
focuses on clinical studies)
² coordination also via the ELIXIR-supported bioschemas.org initiative
² discussion also ongoing under the NIH Commons WGs

33. Mapping to schema.org

34. elements in CEDAR template
v Datasets not yet in a formal
repositories
² CEDAR metadata authoring
tool can be used to provide
DATS-compliant metadata to
be later indexed by DataMed

35. and omicsDI models - Mapping
v Overlap with DATS core
elements
² In red some DATS
extended elements

36. and DCIP supplement - Mapping
Citation metadata for repositories’ landing page

37. https://github.com/datacite/spinone/issues/3
exported by DataCite
v An API endpoint that returns DataCite
metadata in DATS format is work in
progress: http://api.datacite.org/dats
v DataCite Metadata Schema allows for
a RelatedIdentifier with the
HasMetadata relation type
² this allows linking to the DATS
metadata from a DataCite
metadata record