bio-tools/Tool-Information-Standard

Name: Tool-Information-Standard

Owner: bio.tools

Description: An information standard for the description of bioinformatics software tools.

Created: 2018-05-15 10:27:27.0

Updated: 2018-05-15 13:23:10.0

Pushed: 2018-05-15 13:23:08.0

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README

Tool Information Standard

An information standard for the description of bioinformatics software tools.

The standard described below represents a “respectable beta” and will be implemented in https://bio.tools. Please join the discussion on GitHub <https://github.com/bio-tools/biotoolsSchema/issues/77>_

biotoolsSchema <https://github.com/bio-tools/biotoolsSchema/>_ provides the foundation for an information standard for the description of tools that is being adopted by https://bio.tools. The standard has two components:

• a list of tool attributes (see Table below) that must be specified (or stated as not being available) for an entry to be assigned in a 5 tier ratings of entry completeness and quality. Some attributes are grouped (see tables on right) for purposes of determining adherance to the standard.
• a set of Curation Guidelines <http://biotools.readthedocs.io/en/latest/curators_guide.html> describing how each attribute should be specified, i.e. concerning the quality of an entry. The guidelines go beyond the syntactic and semantic constraints defined by biotoolsSchema <https://github.com/bio-tools/biotoolsSchema/>.

Adherence to some of guidelines is verified by automated QC checks within bio.tools, whereas others must be verified by manual inspection.

The standard provides a basis for monitoring of content and labelling of bio.tools entries in various ways:

• entry completeness (“SPARSE” through to “COMPREHENSIVE”)
• whether an entry was manually inspected
• whether an entry is verified, i.e. conforms to the guidelines, passing both the automated and manual checks (stamps of dates of verification and last update would be needed)
• overall entry quality (from “NEEDS TO IMPROVE” through to “EXCELLENT”) conflating notions above (see infographic below)

If and how to use labels is currently under discussion <https://github.com/bio-tools/biotoolsSchema/issues/77>_.

The standard will be applied to bio.tool as follows:

• “SPARSE” : minimum information requirement for new entries. Such entries will be invisible by default (see below) and this made clear to the registrant via the UI.
• “BASIC DETAILS” : level at which an entry becomes visible (by default). Entry visibility will be settable by the user with an option to “Show more results” (i.e. over invisible entries)

.. image:: images/information_standard.png

Why is a standard needed at all?

There are several reasons why a community-defined standard for tool information is helpful:

• accessible summary of what type of information bio.tools provides
• flexible information requirement, including a minimum requirements presenting a low barrier to new registrations, compatible / enabling integration with other major related cataloguing efforts (e.g. BioContainers)
• quality tiers motivate individual entry owners to improve their entries (curation as a “game”), with a “gold standard” of entry quality for curators to aspire to
  
• a framework / workflow to guide tasks and priorities of curators, thematic editors and bio.tools admin
• a basis for metrics of bio.tools quality, KPIs (key performance indicators) of quality improvement objectives, and targets
• a component of branding bio.tools as a trusted source of quality tool information

Description of attributes

Attributes defined as mandatory in the latest stable schema (biotools-2.0.0 <https://github.com/bio-tools/biotoolsSchema/tree/master/versions/biotools-2.0.0>_) are those in the “OKAY” tier plus “Scientific operation” from the “GOOD” tier.

General attributes ^^^^^^^^^^^^^^^^^^ .. csv-table:: :header: “Attribute”, “Description”, “Format”, “element” :widths: 15, 75, 10, 10

“Name“, “Canonical software name assigned by the software developer or service provider”, “Text”, “<name>” “Description“, “Short and concise textual description of the software function”, “Text”, “<description>” “Homepage“, “Homepage of the software, or some URL that best serves this purpose”, “URL”, “<homepage>” “Unique ID“, “Unique ID of the tool that is assigned upon registration of the software in bio.tools”, “Text (URL-safe version of tool name)“, “<toolID>” “Tool type“, “The type of application software: a discrete software entity can have more than one type.“, “enum (from biotoolsSchema, see below)“, “<toolType>” “Scientific topics“, “General scientific domain the software serves or other general category, e.g. 'Proteomics'“, “Term and / or URI of EDAM Topic <http://edamontology.org/topic_0004> concept(s) (1)“, “<topic>” “Publications“, “Publications about the software”, “DOI, PMID or PMCID”, “<publication>” “Scientific operations“, “The basic operation(s) performed by the software, e.g. 'Multiple sequence alignment'“, “Term and / or URI of EDAM Operation <http://edamontology.org/operation_0004> concept(s)“, “<function><operation>” “Operating system“, “The operating system supported by a downloadable software package.“, “enum (from biotoolsSchema)“, “<labels><OperatingSystem>” “Language“, “Name of programming language the software source code was written in, e.g. 'C'.“, “<language>” “License“, “Software or data usage license”, “enum (from biotoolsSchema)“, “<labels><license>” “Type of input & output data“, “Type of primary input / output data (if any), e.g. 'Protein sequences'“, “Term and / or URI of EDAM Data <http://edamontology.org/data_0006> concept(s)“, “<function><input>/<output><data>” “Supported data formats“, “Allowed format(s) of primary inputs/outputs, e.g. 'FASTA'“, “Term and / or URI of EDAM Format <http://edamontology.org/format_1915> concept(s)“, “<function><input>/<output><format>”

"**Scientific benchmark**", "Scientific benchmarking results.", "Link", "``<link><type>Scientific benchmark</type>``"
"**Technical monitoring**", "Technical monitoring results.", "Link", "``<link><type>Technical monitoring</type>``"

“Documentation” group ^^^^^^^^^^^^^^^^^^^^^ .. csv-table:: :header: “Attribute”, “Description”, “Format”, “element” :widths: 15, 75, 10, 10

“General documentation“, “General documentation”, “URL”, “<documentation><type>General</type>” “Manual“, “Information on how to use the software.“, “URL”, “<documentation><type>Manual</type>” “API documentation“, “Human-readable API documentation.“, “URL”, “<documentation><type>API documentation</type>” “API specification“, “File providing an API specification for the software, e.g. Swagger/OpenAPI, WSDL or RAML file.“, “URL”, “<download><type>API specification</type>”

“Code availability” group ^^^^^^^^^^^^^^^^^^^^^^^^^
.. csv-table:: :header: “Attribute”, “Description”, “Format”, “element” :widths: 15, 75, 10, 10

“Repository“, “Link to repository where source code, data and other files may be downloaded”, “URL”, “<link><type>Repository</type>” “Source code“, “Software source code.“, “URL”, “<download><type>Source code</type>” “Source package“, “Source package (of various types) for the software.“, “URL”, “<download><type>Source package</type>”

“Accessibility” group ^^^^^^^^^^^^^^^^^^^^^ .. csv-table:: :header: “Attribute”, “Description”, “Format”, “element” :widths: 15, 75, 10, 10

“Terms of use“, “Rules that one must agree to abide by in order to use a service.“, “URL”, “<link><type>Terms of use</type>” “Accessibility“, “Whether the software is freely available for use.“, “enum (from biotoolsSchema)“, “<labels><Accessibility>” “Cost“, “Monetary cost of acquiring the software.“, “enum (from biotoolsSchema)“, “<labels><Cost>”

“Support” group ^^^^^^^^^^^^^^^^^ .. csv-table:: :header: “Attribute”, “Description”, “Format”, “element” :widths: 15, 75, 10, 10

“Helpdesk“, “Helpdesk providing support in using the software.“, “URL”, “<link><type>Helpdesk</type>” “Issue tracker“, “Link to tracker for software issues, bug reports, feature requests etc.“, “URL”, “<link><type>Issue tracker</type>” “Mailing list“, “Link to mailing list for software announcements, discussions, support etc.“, “URL”, “<link><type>Mailing list</type>” “Contact person“, “Primary contact, e.g. a person, helpdesk or mailing list”, “Name, email, URL and/or ORCID iD”, “<credit><typeRole>Primary contact</typeRole>”

“Downloads” group ^^^^^^^^^^^^^^^^^ .. csv-table:: :header: “Attribute”, “Description”, “Format”, “element” :widths: 15, 75, 10, 10

“Biological data“, “Biological data, or a web page on a database portal where such data may be downloaded.“, “URL”, “<download><type>Biological data</type>” “Binaries“, “Binaries for the software.“, “URL”, “<download><type>Binaries</type>” “Binary package“, “Binary package for the software.“, “URL”, “<download><type>Binary package</type>” “Container file“, “Container file including the software.“, “URL”, “<download><type>Container file</type>” “CWL file“, “Common Workflow Language (CWL) file for the software.“, “URL”, “<download><type>CWL file</type>” “Ontology“, “A file containing an ontology, controlled vocabulary, terminology etc.“, “URL”, “<download><type>Ontology</type>” “VM image“, “Virtual machine (VM) image for the software.“, “URL”, “<download><type>VM image</type>” “Tool wrapper (galaxy)“, “Galaxy tool configuration file (wrapper) for the software.“, “URL”, “<download><type>Tool wrapper (galaxy)</type>” “Tool wrapper (taverna)“, “Taverna configuration file for the software.“, “URL”, “<download><type>Tool wrapper (taverna)</type>” “Tool wrapper (other)“, “Workbench configuration file (other than taverna, galaxy or CWL wrapper) for the software.“, “URL”, “<download><type>Tool wrapper (other)</type>”

.. note:: (1) EDAM is a simple ontology of well established, familiar concepts that are prevalent within bioinformatics, including types of data and data identifiers, data formats, operations and topics. EDAM provides a set of terms with synonyms and definitions - organised into an intuitive hierarchy for convenient use. You can find EDAM on GitHub <https://github.com/edamontology/edamontology>_.