Welcome to biotoolsSchema documentation!¶
This is the documentation for biotoolsSchema.
Contents:
What is biotoolsSchema?¶
biotoolsSchema is a formalised XML schema (XSD) which defines a description model for bioinformatics software. It can be used to describe bioinformatics tools - application software with well-defined data processing functions (inputs, outputs and operations). This includes simple tools with one or a few closely related functions, and complex, multimodal tools with many functions, tools available available for immediate use as online services, or in a form which which you can download, install, configure and run yourself.
biotoolsSchema defines over 50 important scientific, technical and administrative attributes that support cataloguing, discovery, use and interoperability of software. It concentrates upon the salient common features, with a minimal core of 3 attributes only (name, short description and homepage), to provide maximum flexibility for applications. To enable concise information, standard identifiers are used where possible, including EDAM ontology concept IDs for specialised scientific aspects. biotoolsSchema defines 18 controlled vocabularies for technical tool aspects. Verbose information is referred to by URL.
biotoolsSchema together with the EDAM ontology provide the foundation for an information standard for the description of tools. This standard is being adopted by bio.tools and defines the attributes that must be defined within a 5-tier scale of entry completeness and quality.
biotoolsSchema is used by the ELIXIR Tools & Data Services Registry (bio.tools).
How to contribute to biotoolsSchema¶
Contributions to biotoolsSchema are very welcome. Github being our primary communication channel, please do not hesitate to open issues, or comment on them. Pull requests are also welcome! The list of repositories hosting biotoolsSchema and its documentation are listed below. All materials are available under the CC-BY-SA 4.0 license.
Documentation¶
These docs describe the latest stable version (currently 3.0.0) and are maintained in GitHub. Additional documentation is available:
- Technical docs maintained in GitHub where you’ll find example data files
- Usage guidelines including the bio.tools Curators Guide and API Usage Guide
Note
Version 3.0.0 is currently supported in bio.tools.
Status¶
biotoolsSchema is a mature schema having undergone a lot of community-driven revision (e.g. see bio.tools events). Development is use-case driven, primarily by bio.tools. Future versions will not depart fundamentally from the current elements or structure. The development of biotoolsSchema can be followed at GitHub. From version 2.0.0, version numbers follow the MAJOR.MINOR.PATCH pattern:
- MAJOR version for incompatible API changes
- MINOR version for addition of functionality in a backwards-compatible manner
- PATCH version for backwards-compatible bug fixes
Please contribute via GitHub. See also the bio.tools Contributors Guide.
Motivation¶
Bioinformaticians routinely use a large and diverse set of tools and data, and demand powerful and convenient means to organise, find, understand, compare, select, use and connect the available resources. These tasks rely on consistent, machine-understandable resource descriptions. The need - filled by biotoolsSchema - is for an information model that puts the description of a broad range of resources on a consistent syntactic basis.
Citing biotoolsSchema¶
If you use biotoolsSchema, please cite:
Ison J. et al. (2021) biotoolsSchema: a formalized schema for bioinformatics software description. GigaScience, 10 (1)
The article is freely available.
Design considerations¶
The development of biotoolsSchema was guided by the following ten founding principles and design considerations:
- Practical - focus on salient attributes of practical value in everyday use; especially to support the discovery, use and practical interoperability of software; superfluous details are excluded.
- General - generally applicable, i.e. to all manner of bioinformatics resources (see Scope).
- Consistent - use ontologies and standardised enumerations of terms (see Controlled Vocabularies) where possible, to support precise searches over biotoolsSchema-formatted data and return of consistent and therefore comparable information.
- Concise - mandate URLs or standard identifiers where possible, helping to ensure the sustainable upkeep of biotoolsSchema-formatted data and support future integrations, applications and cross-linking with other resources.
- Simple - biotoolsSchema is as flat (unstructured) as is practicable, ensuring ease of use, whilst preserving essential structure, e.g. a meaningful model of tool function.
- Compatible - it is inevitable that tool providers, integrators, and cataloguers will continue to use a variety of models, methods and formats for tool descriptions; biotoolsSchema is broadly compatible (see Comparison to related efforts) to support future integration scenarios.
- Extensible - to cater for emerging requirements, and adaptable by others for their own purposes.
- Stable - the maintenance of software dependencies on mutating schema is expensive. Backwards incompatible changes are only made if absolutely required (see Development process and status).
- Free and open source - to encourage reuse and new applications.
- Community-driven development - to ensure end-user needs are satisfied.
biotoolsSchema elements¶
A summary of elements in biotoolsSchema is below. For more detailed information, please see the technical documentation.
Important
When producing XML files compliant to the schema, it is essential to stick to the element order (including nested elements) as described below. See the sample XML files.
Element groups¶
biotoolsSchema includes scientific, technical and administrative software attributes, organised for convenience into 8 logical groupings (see below).
Note
As of biotoolsSchema 3.3.0, all of the element groups other than “Summary” and “Labels” are reflected as elements/objects in biotoolsSchema/biotoolsSchemaJ.
| Group | XSD element | Description |
|---|---|---|
| Summary | summary | Basic information about the software. |
| Function | function | Details of the function(s) (i.e. modes of operation) the software provides, expressed in terms from the EDAM ontology. |
| Labels | label | Miscellaneous scientific, technical and administrative details of the software, expressed in terms from controlled vocabularies. |
| Links | link | Miscellaneous links for the software e.g. repository, issue tracker or mailing list. |
| Downloads | download | Links to downloads for the software, e.g. source code, virtual machine image or container. |
| Documentation | documentation | Links to documentation about the software e.g. user manual, API documentation or training material. |
| Publications | publication | Publications about the software. |
| Relations | relation | Details of a relationship this software shares with other software registered in bio.tools. |
| Credits | credit | Individuals or organisations that should be credited, or may be contacted about the software. |
Summary group¶
Basic information about the software.
| Element | Description | Type | Cardinality |
|---|---|---|---|
| name | Canonical software name assigned by the software developer or service provider. | xs:token (restriction) | 1 only |
| description | Textual description of the software. | xs:token (restriction) | 1 only |
| homepage | Homepage of the software, or some URL that best serves this purpose. | URL | 1 only |
| biotoolsID | Unique ID (case insensitive) of the tool that is assigned upon registration of the software in bio.tools, normally identical to tool name. | URL (restriction) | 0 or 1 |
| biotoolsCURIE | bio.tools CURIE (compact URI) based on the bio.tools tool ID. | xs:token (restriction) | 0 or 1 |
| version | Version information (typically a version number) of the software applicable to this bio.tools entry. | xs:token (restriction) | 0 or more |
| otherID | A unique identifier of the software, typically assigned by an ID-assignment authority other than bio.tools. | (see below) | 0 or more |
| otherID->value | Value of tool identifier. | xs:token (restriction) | 1 only |
| otherID->type | Type of tool identifier. | enum (see docs) | 0 or 1 |
| otherID->version | Version information (typically a version number) of the software applicable to this identifier. | xs:token (restriction) | 0 or 1 |
Note
See the Curators Guide. As of biotoolsSchema 3.0.0, the Summary group does not have a corresponding element/object in biotoolsSchema/biotoolsSchemaJ (the schema was flattened).
Function group¶
Details of a function (i.e. mode of operation) the software provides, expressed in terms from the EDAM ontology.
Each software entity has one more functions, each corresponding to a mode of operation that the software provides. Each function performs one or more basic operations, and has zero or more primary input and/or output data, each of a specified type and supported format(s). For each operation, data or format element, an EDAM ontology concept URL and/or term are specified.
Data and Format are modelled in the same way as Operation (shown above).
| Element | Description | Type | Cardinality |
|---|---|---|---|
| operation | The basic operation(s) performed by this software function (EDAM Operation). | Ontology concept (restriction) | 1 or more |
| input | Details of primary input data. | ||
| input->data | Type of primary input data (EDAM data). | Ontology concept (restriction) | 1 only |
| input->format | Allowed format(s) of the input data (EDAM Format). | Ontology concept (restriction) | 0 or more |
| output | Details of primary output data. | ||
| output->data | Type of primary output data (EDAM Data). | Ontology concept (restriction) | 1 only |
| output->format | Allowed format(s) of the output data (EDAM Format). | Ontology concept (restriction) | 0 or more |
| operation | data | format->url | URL of an EDAM Operation | Data | Format concept. | URL (restriction) | 0 or 1 |
| operation | data | format->term | An EDAM Operation | Data | Format term (preferred label or synonym). | xs:token | 0 or 1 |
| note | Concise comment about this function, if not apparent from the software description and EDAM annotations. | xs:token (restriction) | 0 or 1 |
| cmd | Relevant command, command-line fragment or option for executing this function / running the tool in this mode. | xs:token (restriction) | 0 or 1 |
Important
The URL must be in the appropriate EDAM Operation | Data | Format namespace, e.g.
- http://edamontology.org/operation_0492
- http://edamontology.org/data_0863
- http://edamontology.org/format_1929
The term, e.g. “Multiple sequence alignment” must be either the preferred label of the concept or a synonym of this term, as defined in EDAM.
Note
See the Curators Guide.
Labels group¶
Miscellaneous scientific, technical and administrative details of the software, expressed in terms from controlled vocabularies.
| Element | Description | Type | Cardinality |
|---|---|---|---|
| toolType | A type of application software: a discrete software entity can have more than one type. | enum (see docs) | 0 or more |
| topic | General scientific domain the software serves or other general category: one of EDAM Topic URL or term is specified. | Ontology concept (restriction) | 0 or more |
| topic->url | URL of an EDAM Topic concept. | URL (restriction) | 0 or 1 |
| topic->term | An EDAM Topic term (preferred label or synonym). | xs:token | 0 or 1 |
| operatingSystem | The operating system supported by a downloadable software package. | enum (see docs) | 0 or more |
| language | Name of programming language the software source code was written in. | enum (see docs) | 0 or more |
| license | Software or data usage license. | enum (see docs) | 0 or 1 |
| collectionID | Tag for a collection that the software has been assigned to within bio.tools. | xs:token (restriction) | 0 or more |
| maturity | How mature the software product is. | enum (see docs) | 0 or 1 |
| cost | Monetary cost of acquiring the software. | enum (see docs) | 0 or 1 |
| accessibility | Whether there are non-monetary restrictions on accessing an online service. | enum (see docs) | 0 or more |
| elixirPlatform | Name of the ELIXIR Platform that is credited. | enum (see docs) | 0 or more |
| elixirNode | Name of the ELIXIR Node that is credited. | enum (see docs) | 0 or more |
| elixirCommunity | Name of relevant ELIXIR (or associated) community. | enum (see docs) | 0 or more |
Note
See the Curators Guide. As of biotoolsSchema 3.0.0, the Labels group does not have a corresponding element/object in biotoolsSchema/biotoolsSchemaJ (the schema was flattened).
Link group¶
Miscellaneous links for the software e.g. repository, issue tracker or mailing list.
| Element | Description | Type | Cardinality |
|---|---|---|---|
| url | A link of some relevance to the software (URL). | URL | 1 only |
| type | The type of data, information or system that is obtained when the link is resolved. | enum (see docs) | 1 or more |
| note | Comment about the link. | xs:token (restriction) | 0 or 1 |
Note
See the Curators Guide.
Download group¶
Links to downloads for the software, e.g. source code, virtual machine image or container.
| Element | Description | Type | Cardinality |
|---|---|---|---|
| url | Link to download (or repo providing a download) for the software. | URL | 1 only |
| type | Type of download that is linked to. | enum (see docs) | 1 only |
| note | Comment about the download. | xs:token (restriction) | 0 or 1 |
| version | Version information (typically a version number) of the software applicable to this download. | xs:token (restriction) | 0 or 1 |
Note
See the Curators Guide.
Documentation group¶
Links to documentation about the software e.g. manual, API specification or training material.
| Element | Description | Type | Cardinality |
|---|---|---|---|
| url | Link to documentation on the web for the tool. | URL | 1 only |
| type | Type of documentation that is linked to. | enum (see docs) | 1 or more |
| note | Comment about the documentation. | xs:token (restriction) | 0 or 1 |
Note
See the Curators Guide.
Publication group¶
Publications about the software
| Element | Description | Type | Cardinality |
|---|---|---|---|
| pmcid | PubMed Central Identifier of a publication about the software. | xs:token (restriction) | 0 or 1 |
| pmid | PubMed Identifier. | xs:token (restriction) | 0 or 1 |
| doi | Digital Object Identifier. | xs:token (restriction) | 0 or 1 |
| type | Type of publication. | enum (see docs) | 0 or more |
| note | Comment about the publication. | xs:token (restriction) | 0 or 1 |
| version | Version information (typically a version number) of the software applicable to this publication. | xs:token (restriction) | 0 or 1 |
Note
See the Curators Guide.
Relation group¶
Details of a relationship this software shares with other software registered in bio.tools.
| Element | Description | Type | Cardinality |
|---|---|---|---|
| biotoolsID | bio.tools ID of an existing bio.tools entry to which this software is related. | xs:token (restriction) | 1 only |
| type | Type of relation between this and another registered software. | enum (see docs) | 1 only |
Note
See the Curators Guide.
Credit group¶
Individuals or organisations that should be credited, or may be contacted about the software.
| Element | Description | Type | Cardinality |
|---|---|---|---|
| name | Name of the entity that is credited. | xs:token (restriction) | 0 or 1 |
| orcidid | Unique identifier (ORCID iD) of a person that is credited. | xs:token (restriction) | 0 or 1 |
| gridid | Unique identifier (GRID ID) of an organisation that is credited. | xs:token (restriction) | 0 or 1 |
| rorid | Unique identifier (ROR ID) of an organisation that is credited. | xs:token (restriction) | 0 or 1 |
| fundrefid | Unique identifier (FundRef ID or Funder ID) of a funding organisation that is credited. | xs:token (restriction) | 0 or 1 |
| Email address. | email address | 0 or 1 | |
| url | URL, e.g. homepage of an institute. | URL | 0 or 1 |
| tel | Telephone number. | xs:token (restriction) | 0 or 1 |
| typeEntity | Type of entity that is credited. | enum (see docs) | 0 or 1 |
| typeRole | Role performed by entity that is credited. | enum (see docs) | 0 or more |
| note | A comment about the credit. | xs:token (restriction) | 0 or 1 |
Note
See the Curators Guide.
Controlled vocabularies¶
biotoolsSchema defines 17 controlled vocabularies - as standarised enumerations of terms - for description of technical software aspects (see below).
| Vocabulary | Description |
|---|---|
| tool type | The type of application software. |
| operating system | The operating system supported by a downloadable software package, e.g. ‘Linux’. |
| programming language | Name of programming language the software source code was written in, e.g. ‘C’. |
| license | Software or data usage license, e.g. ‘GPL-3.0’ |
| maturity | How mature the software product is, e.g. ‘Mature’. |
| cost | Monetary cost of acquiring the software, e.g. ‘Free of charge’. |
| accessibility | Whether there are non-monetary restrictions on accessing an online service, e.g. ‘Open access’. |
| link type | The type of data, information or system that is obtained when the link is resolved, e.g. ‘Helpdesk’. |
| download type | Type of download that is linked to, e.g. ‘Source code’. |
| documentation type | Type of documentation that is linked to, e.g. ‘API documentation’. |
| publication type | Type of publication, e.g. ‘Review’. |
| relation type | Type of relation between this and another registered software, e.g. ‘isNewVersionOf’. |
| entity type | Types of entities that may be credited, e.g. ‘Person’. |
| entity role | Roles that may be assigned to creditable entities, e.g. ‘Developer’. |
| ID type | Type of tool identifier, e.g. ‘rrid’. |
| ELIXIR Platform | Name of the ELIXIR Platform that is credited, e.g. ‘Tools’ |
| ELIXIR Node | Name of the ELIXIR Node that is credited, e.g. ‘Norway’ |
| ELIXIR Community | Name of relevant ELIXIR (or associated) community, e.g. ‘Galaxy’ |
Tool type¶
The type of application software: a discrete software entity can have more than one type, e.g. “Command-line tool, Web application”
| Type | Description |
|---|---|
| Bioinformatics portal |
|
| Command-line tool | A tool with a text-based (command-line) interface. |
| Database portal | A Web site providing a portal to a biological database, typically allowing a user to browse, deposit, search, visualise, analyse or download data. |
| Desktop application | A tool with a graphical user interface that runs on your desktop environment, e.g. on a PC or mobile device. |
| Library | A collection of components that are used to construct other tools. bio.tools scope includes component libraries performing high-level bioinformatics functions but excludes lower-level programming libraries. |
| Ontology | A collection of information about concepts, including terms, synonyms, descriptions etc. |
| Plug-in | A software component encapsulating a set of related functions, which are not standalone, i.e. depend upon other software for its use, e.g. a Javascript widget, or a plug-in, extension add-on etc. that extends the function of some existing tool. |
| Script | A tool written for some run-time environment (e.g. other applications or an OS shell) that automates the execution of tasks. Often a small program written in a general-purpose languages (e.g. Perl, Python) or some domain-specific languages (e.g. sed). |
| SPARQL endpoint | A service that provides queries over an RDF knowledge base via the SPARQL query language and protocol, and returns results via HTTP. |
| Suite | A collection of tools which are bundled together into a convenient toolkit. Such tools typically share related functionality, a common user interface and can exchange data conveniently. This includes collections of stand-alone command-line tools, or Web applications within a common portal. |
| Web application | A tool with a graphical user interface that runs in your Web browser. |
| Web API | An application programming interface (API) consisting of endpoints to a request-response message system accessible via HTTP. Includes everything from simple data-access URLs to RESTful APIs. |
| Web service | An API described in a machine readable form (typically WSDL) providing programmatic access via SOAP over HTTP. |
| Workbench | An application or suite with a graphical user interface, providing an integrated environment for data analysis which includes or may be extended with any number of functions or tools. Includes workflow systems, platforms, frameworks etc. |
| Workflow | A set of tools which have been composed together into a pipeline of some sort. Such tools are (typically) standalone, but are composed for convenience, for instance for batch execution via some workflow engine or script. |
Operating system¶
The operating system supported by a downloadable software package, e.g. “Linux”
| Maturity | Description |
|---|---|
| Linux | All flavours of Linux/UNIX operating systems. |
| Windows | All flavours of Microsoft Windows operating system. |
| Mac | All flavours of Apple Macintosh operating systems (primarily Mac OS X). |
Programming language¶
Name of programming language the software source code was written in, e.g. “C”
See the technical docs for a list of valid terms.
License¶
Software or data usage license, e.g. “GPL-3.0”
See the technical docs for a complete list of valid terms. Noteworthy terms are below:
| License | Description |
|---|---|
| Proprietary | Software for which the software’s publisher or another person retains intellectual property rights - usually copyright of the source code, but sometimes patent rights. |
| Freeware | Proprietary software that is available for use at no monetary cost. In other words, freeware may be used without payment but may usually not be modified, re-distributed or reverse-engineered without the author’s permission. |
| Not licensed | Software which is not licensed and is not proprietary. |
| Other | Software under license not currently supported by biotoolsSchema. |
Maturity¶
How mature the software product is, e.g. “Mature”
| Maturity | Description |
|---|---|
| Emerging | Nascent or early release software that may not yet be fully featured or stable. |
| Mature | Software that is generally considered to fulfill several of the following: secure, reliable, actively maintained, fully featured, proven in production environments, has an active community, and is described or cited in the scientific literature. |
| Legacy | Software which is no longer in common use, deprecated by the provider, superseded by other software, replaced by a newer version, is obsolete etc. |
Cost¶
Monetary cost of acquiring the software, e.g. “Free of charge (with retritions)”
| Cost | Description |
|---|---|
| Free of charge | Software which available for use by all, with full functionality, at no monetary cost to the user. |
| Free of charge (with restrictions) | Software which is available for use at no monetary cost to the user, but possibly with limited functionality, usage restrictions, or other limitations. |
| Commercial | Software which you have to pay to access. |
Accessibility¶
Whether there are non-monetary restrictions on accessing an online service, e.g. “Open access”
| Accessibility | Description |
|---|---|
| Open access | An online service which is available for use to all, but possibly requiring user accounts / authentication. |
| Open access (with restrictions) | An online service which is available for use to all, but possibly with some usage limitations and other restrictions. |
| Restricted access | An online service which is available for use to a restricted audience, e.g. members of a specific institute. |
Link type¶
The type of data, information or system that is obtained when the link is resolved, e.g. “Mailing list”
| Link type | Description |
|---|---|
| Discussion forum | Online forum for user discussions about the software. |
| Galaxy service | An online service providing the tool through the Galaxy platform. |
| Helpdesk | A phone line, web site or email-based system providing help to the end-user of the software. |
| Issue tracker | Tracker for software issues, bug reports, feature requests etc. |
| Mailing list | Mailing list for the software announcements, discussions, support etc. |
| Mirror | Mirror of an (identical) online service. |
| Software catalogue | Some registry, catalogue etc. other than bio.tools where the tool is also described. |
| Repository | A place where source code, data and other files can be retrieved from, typically via platforms like GitHub which provide version control and other features, or something simpler, e.g. an FTP site. |
| Social media | A website used by the software community including social networking sites, discussion and support fora, WIKIs etc. |
| Service | An online service (other than Galaxy) that provides access (an interface) to the software. |
| Technical monitoring | Information about the technical status of a tool. |
| Other | Other type of link for software - the default if a more specific type is not available. |
Download type¶
Type of download that is linked to, e.g. “Binaries”
| Download type | Description |
|---|---|
| API specification | File providing an API specification for the software, e.g. Swagger/OpenAPI, WSDL or RAML file. |
| Biological data | Biological data, or a web page on a database portal where such data may be downloaded. |
| Binaries | Binaries for the software; compiled code that allow a program to be installed without having to compile the source code. |
| Command-line specification | File providing a command line specification for the software. |
| Container file | Container file including the software. |
| Icon | Icon of the software. |
| Screenshot | Screenshot of the software. |
| Source code | The source code for the software, that can be compiled or assembled into an executable computer program. |
| Software package | A software package; a bundle of files and information about those files, typically including source code and / or binaries. |
| Test data | Data for testing the software is working correctly. |
| Test script | Script used for testing testing whether the software is working correctly. |
| Tool wrapper (CWL) | Tool wrapper in Common Workflow Language (CWL) format for the software. |
| Tool wrapper (galaxy) | Galaxy tool configuration file (wrapper) for the software. |
| Tool wrapper (taverna) | Taverna configuration file for the software. |
| Tool wrapper (other) | Workbench configuration file (other than taverna, galaxy or CWL wrapper) for the software. |
| VM image | Virtual machine (VM) image for the software. |
| Downloads page | Web page summarising general downloads available for the software. |
| Other | Other type of download for software - the default if a more specific type is not available. |
Documentation type¶
Type of documentation that is linked to, e.g. “Citation instructions”
| Documentation type | Description |
|---|---|
| API documentation | Human-readable API documentation. |
| Citation instructions | Information on how to correctly cite use of the software; typically which publication(s) to cite, or something more general, e.g. a form of words to use. |
| Code of conduct | A set of guidelines or rules outlining the norms, expectations, responsibilities and proper practice for individuals working within the software project. |
| Command-line options | Information about the command-line interface to a tool. |
| Contributions policy | Information about policy for making contributions to the software project. |
| FAQ | Frequently Asked Questions (and answers) about the software. |
| General | General documentation. |
| Governance | Information about the software governance model. |
| Installation instructions | Instructions how to install the software. |
| Quick start guide | A short guide helping the end-user to use the software as soon as possible. |
| User manual | Information on how to use the software, tailored to the end-user. |
| Release notes | Notes about a software release or changes to the software; a change log. |
| Terms of use | Rules that one must agree to abide by in order to use a service. |
| Training material | Online training material such as a tutorial, a presentation, video etc. |
| Other | Some other type of documentation not listed in biotoolsSchema. |
Publication type¶
Type of publication, e.g. “Primary”
| Publication type | Description |
|---|---|
| Primary | The principal publication about the tool itself; the article to cite when acknowledging use of the tool. |
| Method | A publication describing a scientific method or algorithm implemented by the tool. |
| Usage | A publication describing the application of the tool to scientific research, a particular task or dataset. |
| Benchmarking study | A publication which assessed the performance of the tool. |
| Review | A publication where the tool was reviewed. |
| Other | A publication of relevance to the tool but not fitting the other categories. |
Relation type¶
Type of relation between this and another registered software, e.g. “isNewVersionOf”
| Relation type | Description |
|---|---|
| isNewVersionOf | The software is a new version of an existing software, typically providing new or improved functionality. |
| hasNewVersion | (inverse of above) |
| uses | The software provides an interface to or in some other way uses the functions of other software under the hood, e.g. invoking a command-line tool or calling a Web API, Web service or SPARQL endpoint to perform its function. |
| usedBy | (inverse of above) |
| includes | A workbench, toolkit or workflow includes some other, independently available, software. |
| includedIn | (inverse of above) |
Entity type¶
Type of entity that is credited, e.g. “Person”
| Entity type | Description |
|---|---|
| Person | Credit of an individual. |
| Project | Credit of a community software project not formally associated with any single institute. |
| Division | Credit of or a formal part of an institutional organisation, e.g. a department, research group, team, etc |
| Institute | Credit of an organisation such as a university, hospital, research institute, service center, unit etc. |
| Consortium | Credit of an association of two or more institutes or other legal entities which have joined forces for some common purpose. Includes Research Infrastructures (RIs) such as ELIXIR, parts of an RI such as an ELIXIR node etc. |
| Funding agency | Credit of a legal entity providing funding for development of the software or provision of an online service. |
Entity role¶
Role performed by entity that is credited, e.g. “Developer”
| Role | Description |
|---|---|
| Developer | Author of the original software source code. |
| Maintainer | Maintainer of a mature software providing packaging, patching, distribution etc. |
| Provider | Institutional provider of an online service. |
| Documentor | Author of software documentation including making edits to a bio.tools entry. |
| Contributor | Some other role in software production or service delivery including design, deployment, system administration, evaluation, testing, documentation, training, user support etc. |
| Support | Provider of support in using the software. |
| Primary contact | The primary point of contact for the software. |
ID type¶
Type of tool identifier, e.g. “rrid”
| Role | Description |
|---|---|
| doi | Digital Object Identifier of the software assigned (typically) by the software developer or service provider. |
| rrid | Research Resource Identifier as used by the NIH-supported Resource Identification Portal (https://scicrunch.org/resources). |
| cpe | Common Platform Enumeration (CPE) identifier as listed in the CPE dictionary (https://cpe.mitre.org/dictionary/). |
| biotoolsCURIE | bio.tools CURIE (secondary identifier). |
ELIXIR Platform¶
Name of the ELIXIR Platform that is credited, e.g. “Tools”
| ELIXIR Platform | Description |
|---|---|
| Data | ELIXIR Data Platform |
| Tools | ELIXIR Tools Platform |
| Compute | ELIXIR Compute Platform |
| Interoperability | ELIXIR Interoperability Platform |
| Training | ELIXIR Training Platform |
ELIXIR Node¶
Name of the ELIXIR Node that is credited, e.g. “Norway”
| ELIXIR Node |
|---|
| Belgium |
| Czech Republic |
| Denmark |
| EMBL |
| Estonia |
| Finland |
| France |
| Germany |
| Greece |
| Hungary |
| Ireland |
| Israel |
| Italy |
| Luxembourg |
| Netherlands |
| Norway |
| Portugal |
| Slovenia |
| Spain |
| Sweden |
| Switzerland |
| UK |
ELIXIR Community¶
Name of relevant ELIXIR (or associated) community, e.g. “Galaxy”
| ELIXIR Node |
|---|
| 3D-BioInfo |
| Federated Human Data |
| Galaxy |
| Human Copy Number Variation |
| Intrinsically Disordered Proteins |
| Marine Metagenomics |
| Metabolomics |
| Microbial Biotechnology |
| Plant Sciences |
| Proteomics |
| Rare Diseases |
Contributors¶
Governance¶
biotoolsSchema is a community-driven project governed under the leadership of the French ELIXIR node (Jacques van Helden, Joint Head of Node) in collaboration with other national ELIXIR nodes and partners beyond ELIXIR. biotoolsSchema development is supported by the French ELIXIR node, and has benefited from the voluntary contributions of many individuals since its inception.
Development on the ground is led by French ELIXIR Node staff and affiliates (Hervé Ménager, Jon Ison and Alban Gaignard), in close collaboration with the ELIXIR Tools Platform and other partners within and beyond the ELIXIR infrastructure.
If you’d like to get involved with the project please contact us via GitHub.
Main authors & contributors¶
- Jon Ison (CNRS, Institut Français de Bioinformatique, FR) - lead developer
- Hans-Ioan Ienasescu (University of Copenhagen, DK)
- Emil Rydza (formerly University of Copenhagen, DK)
- Piotr Chmura (University of Copenhagen, DK)
- Kristoffer Rapacki (formerly CBS-DTU, DK)
- Alban Gaignard (L’institut du Thorax, FR)
- Veit Schwämmle (University of Southern Denmark, DK)
- Jacques van Helden (Aix-Marseille Université, FR)
- Matúš Kalaš (University of Bergen, NO)
- Hervé Ménager (Institut Pasteur, FR)
Contributors¶
Thanks to the many people who have contributed - if you’re not listed below, please let us know!
- Dmitry Repchevski (BCS, ES)
- Piotr Wojciech Dabrowski (RKI, DE)
- Bjoern Gruening (University of Freiburg, DE)
- Chris Morris (STFC, UK)
- Frederik Coppens (ELIXIR-BE)
- Heinz Stockinger (ELIXIR-CH)
- Helen Parkinson (EMBL-EBI, UK)
- Julie McMurry (EMBL-EBI, UK)
- Magnus Palmblad (LUMC, NL)
- Michael Crusoe (University of California)
- Niall Beard (University of Manchester)
- Rodrigo Lopez (EMBL-EBI)
- Delegates of the many BioMedBridges and ELIXIR workshops and meetings.
License¶
biotoolsSchema is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License (CC BY-SA 4.0).
We recommend, however, that while biotoolsSchema is being actively maintained by its authors, substantial derived work, major modifications etc. are consulted with the developers beforehand at the time of consideration, and consistent solutions are sought in collaboration.