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Bioschemas Findability and Interoperability.pptx
ChemicalSubstance.shex
ChemicalSubstance_example.json
ChemicalSubstance_example.ttl
DRQ.json
DRQ.ttl
HMDB0001188.json
MolecularEntity.shex
MolecularEntity_example_dopamine.json
MolecularEntity_example_dopamine.ttl
NU000001.json
README.md
chembl-dataset-example.html
molecules.Md

README.md

Adding Bioschemas markup to data repositories and developing tools to find, consume and use it

Presentation

Tasks

1. Creating Markup

Hacking tasks:

Resources:

2. Profile Creation/Refinement

Bioschemas Profile Creation Process

Hacking tasks:

  • Develop missing profiles/type, e.g. Chemistry
    • Need to create new spreadsheet for the crosswalk
  • Refine existing profiles and types, e.g. how to state the position of a Gene in the representation for the Gene
    • Need to create a new version of the crosswalk spreadsheet
  • Improve Bioschemas tutorial material and documentation
  • Prepare schema.org submission for new types and properties

Resources:

3. Developing Support Tools

3.1 GOWeb: Profile Page Generation

3.2 Validata: Markup Validation against Bioschema Profiles

3.3. Buzzbang: Enhancing Search

Representatives:

  • Alasdair Gray
  • Leyla Garcia
  • Ricardo Arcila
  • Phil Barker
  • Michel Dumontier

Achievements

Achievements:

Day 1:

  • Added Bioschemas markup to SynBioHub (DataCatalog, Dataset, DataRecord)
  • Added Bioschemas markup to Bgee (Dataset)
  • Added Bioschemas markup to Hamap (rules, profiles and proteomes Datasets)
  • Updated Bioschemas markup in CathDB (DataCatalog, Dataset, DataRecord)

BioStudies

Ensembl

Chemistry

Community


Bioschemas Community – ELIXIR Interoperability Platform

Background information


Bioschemas is an open community project built on top of schema.org aiming to embed markup in life sciences Web resources to make them more findable and promoting interoperability. Its selling point is its simplicity, with just enough structure in schemas such as ‘DataSet’, ‘BioChemEntity’ and ‘LabProtocol’ to enable FAIRer data applications. Bioschemas markup is being deployed, but more work to develop and exploit it is required.

During the BioHackathon we want to advance development, deployment and exploitation of BioSchemas markup, as well as the tools that enable this. We also want to engage and connect with new groups and communities, such as those working on data indexing, visualization and the semantic web.

Expected outcomes


  1. Markup of core (and other) data resources, including deposition databases, developing new profiles as required
  2. Development of tools supporting: Creation and embedding of markup, Validation of markup
  3. Enhanced searching of life sciences resources based on BioSchemas markup: Crawling and indexing, Generation of life sciences knowledge graph, Rich search results
  4. Training material for development and exploitation of Bioschemas markup using available tools
  5. Publication about Bioschemas

Expected audience


Anyone with ideas about how to get the most of Bioschemas, for instance:

  • Ontologists,
  • Developers with knowledge of JavaScript, Java, GO, Python or other languages are welcome
  • Developers of data resources
  • People interested in web search: data indexing, snippet generation, ranking, etc
  • People interested in RDF and semantic web,
  • Developers interested in Bioschemas applications (data sync, search, knowledge graphs, etc.) Expected hacking days: 4 days

Related works and references


GitHub or any other public repositories of your FOSS products (if any)


Hackers


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