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

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"