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Bioschemas Groups

The following groups, responsible for creating specifications within the project, are active within the Bioschemas community:

  • Beacons - At the moment the registration of a Beacon service in the Beacon Network is done manually and needs to be updated manually if the beacon service changes.
  • Biological Entities - In schema.org we cannot find life science types (eg. protein, gene, biological pathway) except those types that overlap with healthcare and medicine domains defined by the health schema.org extension (eg. drug, artery). These life science types share many elements which can be captured in a common biological entity type.
  • Chemicals - Develop a Bioschemas profile around a chemical use case involving resources such as ChEMBL
  • Community - This project includes many stakeholders and several workstreams. For this project to be successful it will require good communication and coordination, not just among partners but also with the Bioschemas community.
  • Data Repositories - Most Life sciences data repositories are missing a home page providing information about themselves with consistent structured data that would help search engines and registries to index them. Several registries (eg. biosharing, bio.tools, identifiers.org, ...) maintain overlapping efforts to collect certain metadata (eg. title, description, keywords, ...) about “data repositories” (eg. UniProt Knowledgebase, Human Protein Atlas, Protein Data Bank, ...). Most of these registries have a manual curation process There is lack of consistency between the metadata collected by these registries
  • Datasets - Most dataset repositories and registries of dataset do not provide structured data easily crawlable by search engines. Registries like DataMed, OMICsDI and BioSamples do automated ingestion of content mainly through APIs but not all the data repositories have a programmatic interface and the existing variety of programmatic interfaces are subject to changes which break integration workflows.
  • Events - Most dataset repositories and registries of dataset do not provide structured data easily crawlable by search engines. Registries like DataMed, OMICsDI and BioSamples do automated ingestion of content mainly through APIs but not all the data repositories have a programmatic interface and the existing variety of programmatic interfaces are subject to changes which break integration workflows.
  • Genes - In schema.org we cannot find life science types (eg. protein, gene, biological pathway) except those types that overlap with healthcare and medicine domains defined by the health schema.org extension (eg. drug, artery). In previous meetings we discussed the benefits of of Schema.org with several data providers but we also came with a list of concerns that need to be evaluated to be able to encourage data providers to adopt Bioschemas.
  • Laboratory Protocols - In schema.org we cannot find life science types (eg. protein, gene, biological pathway) except those types that overlap with healthcare and medicine domains defined by the health schema.org extension (eg. drug, artery). These life science types share many elements which can be captured in a common biological entity type.
  • Organizations - The Bioschemas Organizations Group develops and maintains a community specification for describing life science organizations.
  • People - Develops and maintains a community specification for describing life science people profiles.
  • Phenotypes - Information of phenotypes is scattered in multiple and disperse samples data repositories. Not all the phenotype data repositories have a programmatic interface and the existing variety of programmatic interfaces are diverse and changeable.
  • Proteins - In schema.org we cannot find life science types (eg. protein, gene, biological pathway) except those types that overlap with healthcare and medicine domains defined by the health schema.org extension (eg. drug, artery). In previous meetings we discussed the benefits of of Schema.org with several data providers but we also came with a list of concerns that need to be evaluated to be able to encourage data providers to adopt Bioschemas.
  • Samples - Information of samples is scattered in multiple and dispersed samples data repositories. Not all the sample data repositories have a programmatic interface and the existing variety of programmatic interfaces are diverse and changeable.
  • Standards - Developing a community specification, based on schema.org, for standards in the Life Sciences.
  • Tools - The Tools Group develops and maintains a community specification for describing life science tools.
  • Training Materials - The Bioschemas Training Materials Group develops and maintains a community specification for describing training materials in biosciences available on the internet.
  • Validation - Though search engines provide validation of the schema.org structured data provided in a page it does not make an analysis of the content of a site and do not validate important features in Bioschemas like compliance with content guidelines, vocabularies or cardinality.

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