Bioschemas Groups Propose a new group

Bioschemas life sciences groups

Active life sciences groups

The following groups, responsible for creating specifications in the Life Science domain, 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.
• Biodiversity - This group aims at specifying profiles and/or types related to the biodiversity domain, starting with the Taxon profile.
• Chemicals - Develop a Bioschemas profile around a chemical use case involving resources such as ChEMBL
• DNA - Representation of DNA concepts such as functional parts (promoters, RBS, terminators, etc), genomic features, and structure (chromosomes, plasmids, etc.)
• Diseases - Develop a Bioschemas profile for diseases and rare diseases.
• 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.
• 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.
• Studies - Properties to support the representation of scientific studies.

Cross-domain groups

Active cross-domain groups

The following groups, responsible for creating corss-domain specifications, are active within 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.
• Laboratory Protocols - The LabProtocols group aims at providing specifications related to studies, for instance protocol and process, as used in a lab, whether wet- or dry-lab. While specifications at the generic level are the initial target, specializations to better cover wet- or dry-lab are also within the scope of this group (either with sub-types or profiles). It is loosely based on the Investigation/Study/Assay (ISA) model.
• Machine Learning - Machine Learning combines data, software, models and workflows. There is a need to harmonize and connect those different elements to have a full picture of a Machine Learning approach from the metadata perspective.
• Scholarly Publications - In schema.org we find multiple types to describe scholarly publications. This group aims to define the profiles for those most relevant for publications in sciences, particularly the Life Sciences.
• Tools - The Tools Group develops and maintains a community specification for describing life science tools.
• Training - The Bioschemas Training Group develops and maintains community specifications for describing training opportunities (face-to-face and online courses) and training resources (permanently accessible materials, videos, slides etc) in the Life sciences.
• Workflow - A workflow consists of an orchestrated and repeatable pattern of activities enabled by the systematic organization of resources into processes that transform materials, provide services, or process information. It can be depicted as a sequence of operations, the work of a person or group, the work of an organization of staff, or one or more simple or complex mechanisms.

Hibernated cross-domain groups

The following groups, responsible for creating corss-domain specifications, are currently hibernating as there has been no activity in at least 6 months. The hibernation could correspond to a maturity reached by all of the specifications supported by the group (i.e., stable types and profiles that have not requrired updates for at least 6 months):

• 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.
• 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.

Supporting groups

These groups provided supporting functions early in the Bioschemas effort. These functions have been now transitioned to the steering commitee. We keep the informatoin here for attribution and legacy purposes:

• 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.
• Standards - Developing a community specification, based on schema.org, for standards in the Life Sciences.
• Technical - The technical group focus on aspects of implementing Bioschemas markup. Please see the Specifications page for the schemas themselves. Please see the software page for tools that can help in publishing or consuming markup.
• 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.