CHANGELOG.md

Changelog for biotoolsSchema

Description of changes are grouped as follows:

• Added: new features
• Changed: changes to existing functionality
• Deprecated: a once-stable feature that has been removed
• Removed: a deprecated feature that has been removed
• Fixed: a bug fix
• Misc: some miscellaneous other change

May 14 2020 biotoolsSchema-3.3.0.xsd release

The major change is some flattening of the schema by removing the <summary> and <labels> elements whose only purpose was to organise / structure the schema. All sub-elements have been preserved and are now nested under <tool>. This change ensures the XML and JSON schema variants of biotoolsSchema have the same structure (so far as possible). For biotoolsSchemaJ (JSON variant) see https://github.com/bio-tools/biotoolsschemaj.

Added

• [198] credit->rorid element added: "Unique identifier (ROR ID) of an organisation that is credited."
• [114] credit->fundrefid element added: "Unique identifier (FundRef ID or Funder ID) of a funding organisation that is credited."
• [178] documentation->type enum extended with Quick start guide: "A short guide helping the end-user to use the software as soon as possible."
• [189] tool->elixirCommunity enum added: "ELIXIR (or other) community to which the software is relevant." See https://biotoolsschema.readthedocs.io/en/latest/controlled_vocabularies.html#elixir-community.
• [195] tool->language enum extended with Elm
• accessibility enum extended with Open access (with restrictions): "An online service which is available for use to all, but possibly with some usage limitations and other restrictions."

Changed

• accessibility redefined to be "Whether there are non-monetary restrictions on accessing an online service." (was "Whether the software is freely available for use") - clarifies the purpose of this field.

Deprecated

Removed

• [196] tool->labels and tool->summary elements removed (sub-elements are now nested under tool element)

Fixed

Misc

• [181] isAvailable global element removed (no longer required)
• [187] download->type of Test data redefined : "Data for testing the scientific performance of the software or whether it is working correctly."

November 25 2019 biotoolsSchema-3.2.0.xsd released

Added

Extensions to enums defining types of things:

• [177] publication->note element added: "Comment about the publication."
• [172] credit->gridid element added: "Unique identifier (GRID ID) of an organisation that is credited." with pattern grid.[0-9]{4,}.[a-f0-9]{1,2 : to support organisational IDs
• [148] credit->orcidid regex pattern now supports http:// (as well as ```https://``)

Other:

• [162] documentation->type enum extended with Code of conduct: "A set of guidelines or rules outlining the norms, expectations, responsibilities and proper practice for individuals working within the software project."
• [152] link->type enum extended with Galaxy service: "An online service providing the tool through the Galaxy platform."
• [149] toolType enum extended with Bioinformatics portal: "A web site providing a platform/portal to multiple resources used for research in a focused area, including biological databases, web applications, training resources and so on." : although not really "tools" this is pragmatic to include (lots of entries in bio.tools match this description).

Changed

Changes to cardinality enabling more precise annotation and simpler==cleaner data:

• [176] publication->type cardinality now 0...many (was 0...1)
• [174] documentation->type cardinality now 1...many (was 1 only)
• [163] link->type cardinality now 1...many (was 1 only)
• [154] accessibility cardinality now 0 or 1 (was 0...many) given there are now two mutually exclusive terms for this value.

Changes to enum values to improve specificity:

• [173] license->type enum changed Unlicensed to Not licensed : to avoid confusion with the Unlicense license
• [167] download->type value of CWL file changed to Tool wrapper (CWL) and redefined to "Tool wrapper in Common Workflow Language (CWL) format for the software." : to make it consistent with the other types of tool wrapper that are supported.
• [166] publication-type enum value Comparison changed to Benchmarking study and redefined as "A publication which assessed the performance of the tool" : makes it more explicit and more useful.
• [156] link-type enum value Registry changed to Software catalogue and redefined as "Some registry, catalogue etc. other than bio.tools where the tool is also described." : makes it clearer.
• [154] license enum value Freeware added "" : "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."
• [151] documentation-type enum value Manual changed to User manual and redefined as "Information on how to use the software, tailored to the end-user." : makes it clearer.

Other changes:

• [148] . character now escaped consistently in all regex patterns.

Deprecated

Removed

Removing enum values to improve scope focus:

• [166] link-type enum value Scientific benchmark removed : it was conflated / redundant with publication->type of Benchmarking study
• [164] download->type enum value Binary package and Source package replaced by Software package defined as "A software package; a bundle of files and information about those files, typically including source code and / or binaries" : to simplify the model / reflect reality better.
• [161] documentation-type enum value Tutorial removed : it was not needed given the general-purpose Training material, which is now redefined as "Online training material such as a tutorial, a presentation, video etc." : out of bitoolsSchema scope to describe all the different types of training material!
• [159] download-type enum value Ontology removed : too much of an edge-case to justify keeping.
• [154] accessibility enum value Proprietary and Freeware removed : it was conflated / redundant with license

Fixed

• [148] labels->license enum value Julia removed (it's a programming language!)

Misc

Redefinition of enum values to make their meaning clearer:

• [155] link-type enum value Helpdesk redefined as "A phone line, web site or email-based system providing help to the end-user of the software." : makes it clearer.
• [164] download->type enum value Binaries redefined as "Binaries for the software; compiled code that allow a program to be installed without having to compile the source code."
• [164] download->type enum value Source code redefined as "The source code for the software, that can be compiled or assembled into an executable computer program."
• [160] documentation->type enum value Citation instructions redefined as "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."
• [157] link->type enum value Repository redefined as "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."
• [153] link->type enum value Service redefined as "An online service (other than Galaxy) that provides access (an interface) to the software."
• [150] toolType enum value Database portal redefined as "A Web site providing a portal to a biological database, typically allowing a user to browse, deposit, search, visualise, analyse or download data."
• [154] accessibility redefined as "Whether an online service is freely available for use."

Other:

• [179] Removed <biotoolsUsage></biotoolsUsage> annotations (in <xs:annotation> elements) indicating whether an element was "Mandatory", "Recommended" etc : this is now redundant as it is handled in the emerging Tool Information Profiles.
• [148] doi regex pattern now consistent wherever it's used (otherId->value and publication->doi).

June 03 2019 biotoolsSchema-3.1.0.xsd released

Added

1. tool->relation elements added: "Details of a relationship this software shares with other software registered in bio.tools."

   • relation->biotoolsID : "bio.tools ID of an existing bio.tools entry which this software is related to."
   • relation->type : "Type of relation between this and another registered software." (isNewVersionOf, hasNewVersion, uses, usedBy, include, includedIn)

2. download->type enum extended:

   • "Other" ("Other type of download for software - the default if a more specific type is not available.")
   • "Downloads page" ("Web page summarising general downloads available for the software.")

3. documentation->type enum extended:

   • "Command-line options" ("Information about the command-line interface to a tool.")
   • "FAQ" ("Frequently Asked Questions (and answers) about the software.")
   • "Release notes" ("Notes about a software release or changes to the software; a change log.")

4. link->type enum extended:

   • "Discussion forum" ("Online forum for user discussions about the software.")
   • "Service" ("An online service that provides access (an interface) to the software.")
   • "Other" ("Other type of link for software - the default if a more specific type is not available.")

Changed

1. summary->homepage is now of urlftptype simpleType (was urltype simpleType) to support those entries (old tools in rare cases) which only have an FTP site for a homepage.

2. function->cmd maxlen facet now 1000 (was 100)

3. labels->elixirPlatform documentation improved : "ELIXIR platform credited for developing or providing the software." (bio.tools tool tip will be improved)

4. labels->elixirNode documentation improved : "ELIXIR node credited for developing or providing the software - the software is in Node Service Delivery Plan." (bio.tools tool tip will be improved)

5. More stringent regex patterns to enforce correct use of fullstop ('.') character (this was not escaped before, meaning any character could be given):

   • urlftptype simpleType as used in linkType complexType (for link->url and documentation->url) and for summary->homepage, download->uri and labels->topic->uri. Regex's are now http(s?)://[^\s/$.?#]*\.[^\s]* and s?ftp://[^\s/$.?#]*\.[^\s]*

   • dataType complexType (as used in function->input->data->uri, function->output->data->uri, function->input->format->uri and function->output->format->uri). Regex is now http://edamontology\.org/data_[0-9]{4}

   • urltype simpleType as used in credit->url. Regex is now http(s?)://[^\s/$.?#]*\.[^\s]*

   • doitype simpleType as used in publication->doi. Regex is now 10\.[0-9]{4,9}[A-Za-z0-9:;\)\(_/.-]+

   • function->operation->uri. Regex is now http://edamontology\.org/operation_[0-9]{4}

   • bio.tools will be refactored if required

6. '''doiType''' simpleType pattern (as used in publication->doi)

   • removed requirement for "doi" or "DOI" prefix (which technically isn't part of the DOI sytnax)
   • enforces correct use of fullstop ('.') character
   • supports [, ], < and > characters
   • Regex are now 10\.[0-9]{4,9}/[A-Za-z0-9:;\)\(_/.-]+ and 10\.[0-9]{4,9}/[\[\]<>A-Za-z0-9:;\)\(_/.-]+ (the second pattern is more restrictive than the first - once we're happy this is OK just this more restrictive one will be needed)
   • bio.tools annotations will be refactored if required

Fixed

1. '''credit->orcidid''' pattern fixed:

   • removed requirement for "http(s?)://orcid.org/" prefix (which isn't part of the ORCID sytnax)
   • added support for terminal 'X' character
   • Regex is now [0-9]{4}-[0-9]{4}-[0-9]{4}-[0-9]{3}[0-9X]
   • bio.tools annotations will be refactored accordingly.

Deprecated

1. link->type enum restricted:

   • "Browser" ("A website for browsing data.") removed. Any existing annotations in bio.tools will be replaced by type "Other".

Misc

1. Pattern restricting a version number now appears in one place only (under versionType) to avoid potential future inconsistencies.

2. Target and default namespace set to "https://bio.tools"

August 01 2018 biotoolsSchema-3.0.0.xsd released

Changes since biotoolsSchema-3.0.0-rc-rev1.xsd released

Changed

1. regex patterns on otherID->value improved:

   • case-insensitie prefixes e.g. "DOI" or "doi"
   • all regex values must be prefixed

2. elixirPlatform moved from credit to labels and is now optional (0 or 1)

3. elixirNode moved from credit to labels and is now optional (0 or 1)

4. Regex pattern of orcidid now supports "http" or "https" prefixes

5. summary->description maxlen facet now 100 (was 500)

6. Schema settings now are:

   • elementFormDefault == qualified
   • attributeFormDefault == qualified
   • No targetNamespace

Removed

1. download->containerFormat removed
2. download->diskFormat removed

March 1 2018 biotoolsSchema-3.0.0-rc-rev1.xsd released

Added

Changed

1. All comment elements renamed to note:

   • credit->note
   • documentation->note
   • download->note
   • link->note
   • function->note

2. credit refactored such that at least one of credit->name, credit->email or credit->url is mandatory.

Deprecated

Removed

1. elixirInfo element grouping removed. These data can be handled internally by ELIXIR Hub (or can be reinstated in future).

2. apiSpec element grouping removed. This can be reinstated as needed.

3. relation element grouping removed. This can be reinstated as needed.

4. isAvailable elements removed: specification of information known to be unavailable (as required by the bio.tools information standard will be handled internally by bio.tools

   • publication->isAvailable
   • link->isAvailable
   • documentation->isAvailable
   • download->isAvailable

5. credit grouping streamlined

   • credit->tel removed
   • credit->gridid removed

6. labels grouping streamlined

   • labels->goTermID removed (will be reinstated as needed)
   • labels->soTermID removed (will be reinstated as needed)
   • labels->taxID removed (will be reinstated as needed)

7. download->cmd removed

8. summary->shortDescription removed

Fixed

Misc

January 26 2018 biotoolsSchema-3.0.0-rc.xsd released

Added

1. isAvailable elements added to support the specification that an attribute is not available for a tool (as required by the bio.tools information standard (https://github.com/bio-tools/biotoolsSchemaDocs/blob/master/information_requirement.rst)

   1.1 publication->isAvailable 1.2 linkType complexType as used in link->isAvailable and documentation->isAvailable 1.3 download->isAvailable

2. summary->otherID added ("A unique identifier of the software, typically assigned by an ID-assignment authority.")

   2.1 summary->otherID->value (1 only), minlen facet of 1, is the value of the identifier (with appropriate regexs as per type, see below) 2.2 summary->otherID->type (0 or 1) is enum of the identifier type (doi, rrid, cpe, biotoolsID) 2.3 summary->otherID->version (0...1) (see below)

3. Version information refactored

   3.1 New versionType simpleType 3.2 xs:token with facets minlen (1), maxlen (100) 3.3 preserving pattern facet previously defined in summary->version

4. Version elements added:

   4.1 summary->otherID->version (0...1) ("Version information (typically a version number) of the software applicable to this identififier.") 4.2 download->version (0...1) added ("Version information (typically a version number) of the software applicable to this download.") 4.3 publication->version (0...1) added ("Version information (typically a version number) of the software applicable to this publication.")

5. summary->biotoolsCURIEadded

   5.1 0...1 cardinality 5.2 type of xs:anyURI 5.3 regex is biotools:[_a-zA-Z][_\-.0-9a-zA-Z]*

6. function->cmd added ("Relevant command, command-line fragment or option for executing this function / running the tool in this mode.")

   6.1 Type is xs:token 6.2 minLen facet of 1 6.3 maxLen facet of 100

7. link->type enum extended:

   7.1 "Scientfic benchmark" ("Information about the scientific performance of a tool." 7.2 "Technical monitoring" ("Information about the technical status of a tool."

8. documentation->type enum extended:

   8.1 "Governance" ("Information about the software governance model.") 8.2 "Contributions policy ("Information about policy for making contributions to the software project.") 8.3 "Installation instructions" ("Instructions how to install the software.") 8.4 "Tutorial" ("A tutorial about using the software.") 8.5 Governance added to documentation->type enum

9. labels->license enum extended with "Unlicensed" value

Added / changed

1. publication->type enum, mulitple modifications:

   1.1 "Primary" (no change) The principal publication about the software itself; the article to cite when acknowledging use of the software. 1.2 "Method" (new!) A publication describing a scientific method or algorithm implemented by the software. 1.3 "Usage" (new!) A publication describing the application of the software to scientific research, a particular task or dataset. 1.4 "Comparison" (was "Benchmark") A publication which assessed the performance of the software relative to other tools. 1.5 "Review" (no change) A publication where the software was reviewed. 1.6 "Other" (no change)

Changed

1. Elements that were mandatory are now optional:

   1.1 function (now 0...many) 1.2 labels->toolType (now 0...many) 1.3 labels->topic (now 0...many) 1.4 labels (now 0...1)

2. credit element group refactored (merging in attributes from old contact element group)

   2.1 Annotation chaned to "An individual or organisation that should be credited, or may be contacted about the software." 2.2 credit->elixirPlatform and credit->elixirNode added (moved from elixirInfo). In a credit one must specify 1) an ELIXIR platform or node name or 2) a credit with a name, a mandatory ID/means of contact and optional type and role (see the schema docs) 2.3 credit->tel (telephone number) added ( minlen facet of 5, maxlen facet of 50) 2.4 credit->typeRole cardinality changed to 0...many (was 0...1) 2.5 credit->typeRole enum extended with "Primary contact" to indicate this credit is a primary contact for the software. 2.6 credit->orcidId changed to credit->orcidid 2.7 credit->gridId changed to credit->gridid 2.8 credit->name now xs:token (was nameType simple type) 2.9 credit->url now of urlTyp simpleType

3. download->cmd refactored

   3.1 xs:token (was textType simple type) 3.2 minLen facet set to 1 3.3 maxLen facet set to 100

4. biotoolsIdType refactored

   4.1 minLen facet removed (redundant). 4.2 maxLen facet removed

5. relation->biotoolsID refactored

   5.1 type changed from biotoolsUrlType to biotoolsIdType simple type 5.2 name changed to biotoolsID

6. collectionID refactored

   6.1 type changes to nameType simpleType (was biotoolsCollectionIdType simpleType) 6.2 minlen facet to 1, maxlen to 50

7. Changes to elements in summary group:

   7.1 summary->name element maxlen facet set to 100. 7.2 summary->version now 0...many (was 0 or 1) 7.3 summary->description maxlen facet now 500 (was 50) 7.4 summary->shortDescription maxlen facet now 100 (enforcing that the short desriptions really must be short!) 7.5 summary->shortDescription type set to textType (was xs:token) 7.6 summary->toolid renamed to summary->biotoolsID

8. linkType->comment type set to textType (consistent with other free-text comments) (linkType is complex type used by link->comment and documentation->comment elements)

9. doiType simpleType and "pmid" global element refactored, to drop support for PMIDs and DOIs with "PMID:" and "DOI:" prefix respectively (regex```s changed)

Removed

1. summary->doi (use instead summary->otherID->value and set summary->otherID->type = doi)
2. summary->versionID (this no longer supported by bio.tools)
3. contact element grouping removed (the refactored credit should be used instead)
4. biotoolsCollectionIdType simpleType (no longer used)
5. biotoolsUrlType simpleType (no longer used)

Fixed

1. credit->email duplicate pattern restriction removed

November 17, 2016 biotoolsSchema-2.0.0.xsd released

Sorry, no bandwidth to provide summary of changes : please see the schema documentation. changelog will be maintained properly henceforth!

November 8, 2016 biotoolsSchema-2.0-beta04.xsd released

Sorry, no bandwidth to provide summary of changes : please see the schema documentation.

November 3, 2016 biotoolsSchema-2.0-beta03.xsd released

Sorry, no bandwidth to provide summary of changes : please see the schema documentation.

October 22, 2016 biotoolsXSD officially renamed to biotoolsSchema, biotoolsSchema-2.0-beta02.xsd released

Sorry, no bandwidth to provide summary of changes : please see the schema documentation.

August 12, 2016 biotoolsXSD-2.0-beta01.xsd released

A complete revision of the schema. Too many changes to list, therefore the highlights only are summarised below. For more information please read the schema documentation.

Added : new or restructured element groupings (see schema docs for details)

1. summary: "Basic information about the software."
2. function: "Details of the function(s) that this software provides, expressed in terms from the EDAM ontology."
3. labels: "Miscellaneous scientific, technical and administrative details of the software, expressed in terms from controlled vocabularies."
4. relation: "Details of a relationship this software shares with other software registered in bio.tools."
5. commandLineSpec: "Details of the command-line interface to a tool, if appropriate."
6. apiSpec: "Details of the API to a service, if appropriate, including service endpoints."
7. image: "Details for a virtual machine image or container for the software."
8. download: "Link to a miscellaneous download for the software, e.g. source code." A controlled vocabulary for download types is defined.
9. documentation: "A link to documentation about the software including training materials." A controlled vocabulary for documentation types is defined.
10. publication: "A publications about the software.". A controlled vocabulary for publication types is defined.
11. contact: "Details of a contact for the software, e.g. developer or helpdesk." A controlled vocabulary for contact types/roles is defined.
12. credit: "An individual or organisation that should be credited for the software."

Added : new elements

1. biotoolsID: "Unique ID that is assigned upon registration of the software in bio.tools."
2. doi: "Canonical Digital Object Identifier of the software assigned by the software developer or service provider."
3. shortDescription: "Short and concise textual description of the software function."
4. repository: "Repository where source code, data and other files may be downloaded."
5. socialMedia: "A website used by the software community including social networking sites, discussion and support fora, WIKIs etc."
6. function->comment: " Concise textual description of the function(s), if this is not already obvious from the resource description."
7. goTermID: "Gene function including molecular function, cellular component and biological process. Miscellaneous ontology annotation. The ID of Gene Ontology (GO) concept(s) are specified."
8. soTermID: Features which can be located on a biological sequence. The ID of Sequence Ontology (SO) concept(s) are specified.
9. taxId: NCBI taxonomy ID of taxonomic group the software (particularly database portals) caters for.
10. status: Label describing miscellaneous status of the software." A controlled vocabulary is defined.
11. credit->orcidId : "Unique identifier (ORCID iD) of a person that is credited."
12. credit->gridId : "Unique identifier (GRID ID) of an organisation that is credited."

Added : new enum values

1. New values to enum:

   • "Other"
   • "Proprietary"
   • "Common Development and Distribution License (CDDL-1.0)"

2. New values to enum:

   • "AWK"
   • "MATLAB"
   • "JSP"
   • "PyMOL"

Changed : element name changes

1. resources -> tools
2. resource -> tool
3. functionName -> operation
4. resourceType -> toolType
5. platform -> operatingSystem

Changed : other

1. operation, data, format and topic elements now include uri and term elements.
2. collection : now restricted to accept a bio.tools ID of a software collection, rather than free-text.

Removed

1. publications element group replaced by publication with new structure.
2. uses element group replaced by relation.
3. interface element group removed, now handled by download and documentation. Note that interfaceType is removed completely (now subsumed in toolType).
4. elixirInfo element group, maturity and cost removed, now handled by status.
5. docs element group replaced by documentation.
6. credits element group replaced by credit.
7. canonicalID replaced by doi.
8. accessibility now handled via status.
9. tag removed: annotations are now restricted to controlled vocabulary terms defined in labels.
10. functionHandle and dataHandle removed, now handed by commandLineSpec.
11. functionDescription and dataDescription removed, now handled by function->comment.
12. sourceRegistry removed, now handled by collection.

October 17th, 2015 biotoolsXSD-1.4.xsd released

Added

• New docs->docsDownloadSource optional element : "Source code downloads page (URL)"
• New docs->docsDownloadBinaries optional element : "Software binaries downloads page (URL)"
• New docs->docsGithub optional element : "Github page (URL)"
• "Maintainer" added to contactRole enum
• "Other" added to ```resourceType" enum

Changed

• publications is now optional
• functionHandle element maxLen facet increased to 300 (via maxLen facet on name simpleType; also set to 300)
• Parentheses added to pattern restriction on name element, which is now [\p{Zs}A-Za-z0-9+.,-_:;()]*

Misc

• docsDownload purpose changed from "Software or data downloads page (URL)" to "General downloads page (URL)"

September 22nd, 2015 biotoolsXSD-1.3.xsd released

Added

• "Artistic License 2.0" added to license enum
• "Icarus" added to language enum
• id attribute added to resource element. This is the unique ID (URI) of the resource.
• Default value of "None" added to publicationsPrimaryID and publicationsOtherID

Changed

safe changes:

• name element maxLen facet restriction increased to 200 characters
• + added to name simpleType pattern restriction, which is now [\p{Zs}A-Za-z0-9+.,-_:;]*

potentially breaking change:

• maturity element enum values changed to:

  • "Early" (was "Nascent" or "Young" in biotoolsXSD 1.2)
  • "Stable" (was "Established" in biotoolsXSD 1.2)
  • "Deprecated" (was "Retiring" or "Extinct" in biotoolsXSD 1.2)

• platform enum value "Unix" removed (use "Linux" instead)

• resourceType element enum values removed: "Dataset", "Tool (query and retrieval), "Tool (analysis)", "Tool (deposition)", "Tool (visualiser)", "Tool (utility)", "Suite", "Framework", "Virtual machine", "Widget" and "Other"

• New resourceType enum values are as follows:

  • "Database" (was "Database" or "Dataset" in biotoolsXSD 1.2)
  • "Tool" (was "Tool", "Tool (query and retrieval), "Tool (analysis)", "Tool (deposition)", "Tool (visualiser)", "Tool (utility)" or "Workflow" in biotoolsXSD 1.2)
  • "Service" (new in biotoolsXSD 1.3)
  • "Workflow" (no change)
  • "Platform" (new in biotoolsXSD 1.3, was "Framework" or "Suite" in biotoolsXSD 1.2)
  • "Container" (new in biotoolsXSD 1.3, was "Virtual machine" in biotoolsXSD 1.2
  • "Library" (was "Library" or "Widget" in biotoolsXSD 1.2)

• The definition of these resource types are:

  • "Database" - A collection of data, datasets, a registry etc.
  • "Tool" - Software which you can download, install, configure and run yourself.
  • "Service" - Software provided as a service and available for immediate use, e.g. on the Web.
  • "Workflow" - A definition of a collection of tools, services etc. for running in a workflow system.
  • "Platform" - An integrated environment, including suites, workbenches, workflow systems, frameworks etc.
  • "Container" - A collection of data, tools, services etc. in a portable environment, e.g. VMs, Docker.
  • "Library" - A package of code for building/extending tools, including widgets, plug-ins, toolkits etc.

• interfaceType element enum values removed: "REST API", "URL", "SQL" and "SPARQL"

• New interfaceType enum values are as follows:

  • "Command-line" (no change)
  • "Web UI" (no change)
  • "Desktop GUI" (no change)
  • "SOAP WS" (no change)
  • "HTTP WS" (new in biotoolsXSD 1.3, was "REST API" or "URL" in biotoolsXSD 1.2)
  • "API" (no change)
  • "QL" (new in biotoolsXSD 1.3, was "SQL" or "SPARQL" in biotoolsXSD 1.2)

• The definition of these interface types are:

• "Command line" - Text-based interface to a tool or service.

  • "Web UI" - Graphical user interface available on the Web.
  • "Desktop GUI" - Graphical user interface that runs on your own machine.
  • "SOAP WS" - Programmatic access provided via SOAP and WSDL file.
  • "HTTP WS" - Access provided via HTTP, including simple URLs, RESTful APIs etc.
  • "API" - Application programmers interface to a programming library. " "QL" - Query language interface to a database, e.g. SQL, SPARQL etc.

Deprecated

• Use of the tag element is deprecated and will be removed in a future version.

Removed

Fixed

Misc

June 8th, 2015 biotoolsXSD-1.2.xsd released

Added

• Bash added to enum of language element
• tag maxlen facet set to 50

Changed

• maxLen facet restriction on all elements of type Text removed (was 512), such that the length restriction of 1000 (defined on Text) applies
• Single space added to Name simpleType pattern restriction, which is now [\p{Zs}A-Za-z0-9.,-_:;]*
• The following elements (all simpleType) changed type to simpleType Name:
  • collection
  • usesName
  • function->input/output->dataHandle
  • elxirInfo->elixirStatus
  • elxirInfo->elixirNode
  • function->functionHandle

potentially breaking change:

• tag element (was complexType ontologyTerm) also changed to simpleType "Name"

May 5th, 2015 biotoolsXSD-1.1.xsd released

Added

• "accessibility" (optional) added: whether resource is accessible to all or not: enum of "Public" or "Private"
• New simple type URLFTP which is URL supporting FTP URLs

Changed

• publications (1 max.) is now mandatory, publications->publicationsPrimaryID is now mandatory (1 max.)
• "None" value added to valid patterns for CitationID simpleType, i.e. publications->publicationsPrimaryID may have a value of "None" if PMID, PMCID or DOI is not available.
• Name element pattern restriction added: [A-Za-z0-9.,-_:;]*
• Name element maxLen facet restriction reduced from 100 to 50 characters
• "Dataset" value added to enum of resourceType
• docs->docsDownload type changed to URLFTP from URL
• docs->docsCitationInstructions changed to URLFTP from URL
• docs->docsTermsOfUse changed to URLFTP from URL
• interface->interfaceDocs changed to URLFTP from URL
• resourceType type changed to Name simpleType (enum of permitted values preserved)
• interfaceType type changed to Name simpleType (enum of permitted values preserved)
• maturity type changed to Name simpleType (enum of permitted values preserved)
• platform type changed to Name simpleType (enum of permitted values preserved)
• language type changed to Name simpleType (enum of permitted values preserved)
• license type changed to Name simpleType (enum of permitted values preserved)
• cost type changed to Name simpleType (enum of permitted values preserved)
• description maxLen facet restriction reduced from 1000 to 512 characters
• function->functionDescription maxLen facet restriction reduced from 1000 to 512 characters
• function->input/output->dataDescription maxLen facet restriction reduced from 1000 to 512 characters

Fixed

• language enum value of "C Shapr" changed to "C#"
• language enum value of "Assembly" changed to "Assembly language"
• language enum value of "Methematica" changed to "Mathematica"
• language enum value of "R changed to "R"