GitHub Twitter

Bioschemas Groups

A list of the teams responsible for creating specifications within the Bioschemas project.

The following groups 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.

Group Leaders

Serena Scollen

Audald Lloret

Objectives
  1. Expose Beacon service metadata in its default landing web page with Bioschemas
  2. Automate the ingestion of the beacon service metadata into the Beacon Network
Specifications




Biodiversity

This group aims at specifying profiles and/or types related to the biodiversity domain, starting with the Taxon profile.

Group Leaders

Franck Michel

Leyla Garcia

Objectives
  1. Define the main characteristics of a Taxon as a Bioschemas profile
  2. Make biodiversity-related web portals and data registries more findable using search engines
  3. Facilitate the linking to major web portals and data registries such as GBIF, Enciclopedia of Life, Catalogue of Life
  4. Engage and help the biodiversity community to test and adopt the exposure of biodiversity markkup




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.

Group Leaders

Carlos Horro

Leyla Garcia

Philippe Rocca-Serra

Objectives
  1. Describe biological entities using Bioschemas compliant markup so biological types can be more easily indexed by search engines and registries.
  2. Evaluating the issues and benefits about how to work with biological entities in schema.org and Bioschemas
Specifications




Chemicals

Develop a Bioschemas profile around a chemical use case involving resources such as ChEMBL

Group Leaders

Michał Nowotka

Objectives
  1. Test the adoption of schema.org around a chemical use case involving chemical resources such as ChEMBL.
  2. Evaluating the issues and benefits about how to work with schema.org and Bioschemas.




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.

Group Leaders

Carole Goble

Alasdair Gray

Objectives
  1. Provide support, facilitate communication and engage not just project partners but the community including Bioschemas and other related efforts like Force11 and BD2K
  2. Produce and enhance documentation to facilitate the adoption of Bioschemas from a technical perspective
  3. Provide project coordination
  4. Make sure there is alignment among workstreams as well as alignment among specifications
  5. Make sure there is a common set of minimum properties that facilitates contextualisation
  6. Coordinate with the ELIXIR interoperability platform and external partners




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

Group Leaders

Henning Hermjakob

Objectives
  1. Describe data repositories using Bioschemas compliant markup so data repositories can be more easily indexed by search engines and registries.
  2. Evaluate how registries should collect structured metadata exposed by data repositories to facilitate an automatic or semiautomatic update their records and present more consistent descriptions.
  3. Explore how to collect structured metadata for some of the metrics proposed by the ELIXIR data platform.
Specifications




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.

Group Leaders

Susanna A Sansone

Objectives
  1. Facilitate the ingestion of datasets metadata from data repositories (databases) into search engines and dataset registries like OMICsDI and DataMed via Bioschemas
  2. Automate the linking of datasets metadata to samples in dataset registries like Biosamples, and identify cases where samples are missing or metadata is absent.
  3. Engage and help data providers to test and adopt the exposure of dataset metadata Bioschemas
  4. Contribute to increase the number of indexed data repositories via Bioschemas.
  5. Make dataset registries compliant with Bioschemas.
Specifications




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.

Group Leaders

Martin Cook

Objectives
  1. To develop a common schema to facilitate the description and dissemination of life science events, using schema.org.
  2. To create a specification that includes a metadata schema, minimum information guidelines and recommended vocabularies. It should also include documentation and examples about how to use the event schema.
  3. To engage the people that are interested in describing life science events to participate and shape the specification.
Specifications




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.

Group Leaders

Leyla Garcia

Objectives
  1. Test the adoption of schema.org around a gene use case involving gene resources.
  2. Evaluating the issues and benefits about how to work with schema.org and Bioschemas
Specifications




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.

Group Leaders

Olga Ximena Giraldo

Objectives
  1. Describe biological laboratory protocols using Bioschemas compliant markup so protocols can be more easily indexed by search engines and registries.
  2. Evaluating the issues and benefits about how to work with laboratory protocols in schema.org and Bioschemas
Specifications




Organizations

The Bioschemas Organizations Group develops and maintains a community specification for describing life science organizations.

Group Leaders

Rafael C Jimenez

Richard Holland

Objectives
  1. To develop a common schema to facilitate description and dissemination of life science organizations as an extension of schema.org.
  2. To create a specification including a metadate schema, minimum information guidelines, recommended vocabularies as well as documentation and examples about how to use the schema.
  3. To engage the community interested to describe file science organizations to participate and shape the specification.
Specifications




People

Develops and maintains a community specification for describing life science people profiles.

Group Leaders

Objectives
  1. To develop a common schema to facilitate description and dissemination of life science people profiles as an extension of schema.org.
  2. To create a specification including a metadata schema, minimum information guidelines, recommended vocabularies as well as documentation and examples about how to use the schema.
  3. To engage the community interested to describe file science people profiles to participate and shape the specification.
Specifications




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.

Group Leaders

Carlos Horro

Objectives
  1. Relay on the metadata description defined by the ELIXIR plant use case
  2. Automate the ingestion of sample metadata from phenotype data repositories into registries via Bioschemas.
  3. Engage and help data providers to test and adopt the exposure of phenotype metadata with Schema.org via Bioschemas.
  4. Make registries like TransPlant compliant with Schema.org via Bioschemas.
  5. Focus on plant phenotypes but consider a general definition of phenotype taking into account different types of phenotypes. eg. biomedical phenotypes, mouse phenotypes, ...




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.

Group Leaders

Maria Martin

Objectives
  1. Test the adoption of schema.org around a protein use case involving protein resources.
  2. Evaluating the issues and benefits about how to work with schema.org and Bioschemas
Specifications




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.

Group Leaders

Helen Parkinson

Tony Burdett

Objectives
  1. Facilitate the ingestion of sample metadata from data repositories (eg. Biobank databases) into registries like the Biosamples, BBMRI Biobank directory or the UKCRC Tissue Directory via Bioschemas.
  2. Engage and help data providers and developers of BioBank LIMS to test and adopt the exposure of sample metadata via Bioschemas
  3. Contribute to contextualise information from data sample registries (eg. Biosamples) and biobank sample repositories (eg. NL Biobank) and Biobank Registries (eg. BBMRI Biobank directory)
  4. Make registries like Biosamples compliant with Bioschemas.
Specifications




Standards

Developing a community specification, based on schema.org, for standards in the Life Sciences.

Group Leaders

Peter McQuilton

Objectives
  1. Develop a specification for how to use schema.org to describe standards within the Life Sciences.
Specifications




Technical

The technical group focus on aspects of implementing Bioschemas markup. Please see the Specifications page for the schemas themselves. Please see the tools page for tools that can help in publishing or consuming markup.

Group Leaders

Justin Clark-Casey

Objectives




Tools

The Tools Group develops and maintains a community specification for describing life science tools.

Group Leaders

Giuseppe Profiti

Objectives
  1. This group investigates the required extensions to schema.org to support such use case.
Specifications




Training Materials

The Bioschemas Training Materials Group develops and maintains a community specification for describing training materials in biosciences available on the internet.

Group Leaders

Niall Beard

Gabriella Rustici

Objectives
  1. To develop a common schema to facilitate the description and dissemination of life science training material, using schema.org.
  2. To define a set of metadata and vocabularies, built on top of existing technologies and standards, that can be used to represent training materials in web pages and applications.
  3. To make it easier to discover, exchange and integrate life science training material information across the internet.
Specifications




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.

Group Leaders

Alasdair Gray

Objectives
  1. Provide a GUI to validate Bioschemas compliant websites and Bioschemas compliant sites
  2. Validate data repositories adopting Bioschemas



Top ▲