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Utility for verification of bio.tools content with reporting
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README.md

README.md

What is biotoolsLint?

biotoolsLint is under design : coding has not started and this page may be missing information

biotoolsLint is a utility for verification and reporting of content of the ELIXIR Tools & Data Services Registry. It will, for purposes of content quality control and labelling, verify the content according to:

  • tool description syntax defined by biotoolsSchema
  • correct or recommended use of the EDAM ontology
  • curation best practice from the bio.tools Curators Guide (in so far as these recommendations can be automatically verified)
  • compliance to the Tool Information Standard
  • miscellaneous other checks, e.g. broken link detection, tool name uniqueness etc.

Verifications

The verifications are exhaustively tabulated below, including one table / element group defined in biotoolsSchema.

Element-specific verifications

summary group

General verifications

Summary group

See schema docs & curators guide

summary group

otherid

Verification Log level Issue Status
name: API usage, curators guide
Invalid cardinality (1 only allowed) ERROR 33 tbd
Name is taken (not unique within bio.tools) ERROR 30 tbd
Invalid syntax (disallowed characters) WARN 37 tbd
Invalid syntax (disallowed whitespace) WARN 40 tbd
Invalid syntax (length) WARN 36 tbd
Includes technical jargon WARN 31 tbd
Includes version or status info WARN 26 tbd
Name similarity (full-length exact match to substring of existing tool name) INFO 32 tbd
description: API usage, curators guide
Invalid cardinality (1 only allowed) ERROR 33 tbd
Invalid syntax (disallowed whitespace) WARN 40 tbd
Invalid syntax (length) WARN 36 tbd
Wrong or missing capitalisation and full stops WARN 35 tbd
Includes DOI(s) WARN 28 tbd
Includes URL(s) WARN 27 tbd
homepage: API usage, curators guide
Invalid cardinality (1 only allowed) ERROR 33 tbd
Invalid syntax (pattern) ERROR 34 tbd
Broken link WARN 12 tbd
Uses existing tool homepage URL WARN 38 tbd
biotoolsID: API usage, curators guide
Mismatch of biotoolsID & biotoolsCURIE WARN 22 tbd
biotoolsCURIE: API usage, curators guide
Mismatch of biotoolsID & biotoolsCURIE WARN 22 tbd
version: API usage, curators guide
Invalid syntax (disallowed characters) WARN 37 tbd
Invalid syntax (disallowed whitespace) WARN 40 tbd
Invalid syntax (length) WARN 36 tbd
otherID: API usage, curators guide
otherID->value
Invalid syntax (pattern) ERROR 34 tbd
otherID->type
Invalid value (must adhere to controlled vocabulary) ERROR 39 tbd
otherID->version
Invalid syntax (disallowed characters) WARN 37 tbd
Invalid syntax (length) WARN 36 tbd

Function group

See schema docs & curators guide

function group

operation

Verification Log level Issue Status
operation: API usage, curators guide
operation->uri
Placeholder EDAM concept (not normally used for annotation) WARN 10 tbd
Deprecated EDAM concept WARN 6 tbd
Duplicated operation ERROR 3 tbd
Undefined Operation::Topic relation INFO 41 tbd
Missing input INFO 42 tbd
Missing output INFO 43 tbd
operation->term
Invalid term ERROR 7 tbd
Use of synonym INFO 8 tbd
input|output->data: API usage, curators guide
input|output->data->uri
Placeholder EDAM concept (not normally used for annotation) WARN 10 tbd
Deprecated EDAM concept WARN 6 tbd
Undefined Data::Topic relation INFO 41 tbd
Undefined Data::Operation relation INFO 41 tbd
data->term
Invalid term ERROR 7 tbd
Use of synonym INFO 8 tbd
input|output->format: API usage, curators guide
input|output->format->uri
Placeholder EDAM concept (not normally used for annotation) WARN 10 tbd
Deprecated EDAM concept WARN 6 tbd
Duplicated format ERROR 3 tbd
Undefined Data::Format relation WARN 41 tbd
format->term
Invalid term ERROR 7 tbd
Use of synonym INFO 8 tbd
note: API usage, curators guide
Invalid syntax (disallowed whitespace) WARN 40 tbd
Invalid syntax (length) WARN 36 tbd
cmd: API usage, curators guide
Invalid syntax (disallowed whitespace) WARN 40 tbd
Invalid syntax (length) WARN 36 tbd

See also the general EDAM verifications.

Labels group

See schema docs & curators guide

labels group

Verification Log level Issue Status
toolType: API usage, curators guide
Invalid value (must adhere to controlled vocabulary) ERROR 39 tbd
Duplicated toolType ERROR 4 tbd
topic: API usage, curators guide
topic->uri
Duplicated topic ERROR 3 tbd
Placeholder EDAM concept (not normally used for annotation) WARN 10 tbd
Deprecated EDAM concept WARN 6 tbd
topic->term
Invalid term ERROR 7 tbd
Use of synonym INFO 8 tbd
operatingSystem: API usage, curators guide
Invalid value (must adhere to controlled vocabulary) ERROR 39 tbd
Duplicated operatingSystem ERROR 4 tbd
language: API usage, curators guide
Invalid value (must adhere to controlled vocabulary) ERROR 39 tbd
Duplicated language ERROR 4 tbd
license: API usage, curators guide
Invalid value (must adhere to controlled vocabulary) ERROR 39 tbd
collectionID: API usage, curators guide
Invalid value (must adhere to controlled vocabulary) ERROR 39 tbd
Duplicated collectionID ERROR 4 tbd
maturity: API usage, curators guide
Invalid value (must adhere to controlled vocabulary) ERROR 39 tbd
cost: API usage, curators guide
Invalid value (must adhere to controlled vocabulary) ERROR 39 tbd
accessibility: API usage, curators guide
Invalid value (must adhere to controlled vocabulary) ERROR 39 tbd
Duplicated accessibility ERROR 4 tbd

Links group

See schema docs & curators guide

labels group

Verification Log level Issue Status
url: API usage, curators guide
Invalid syntax (pattern) ERROR 34 tbd
Broken link WARN 12 tbd
type: API usage, curators guide
Invalid value (must adhere to controlled vocabulary) ERROR 39 tbd
note: API usage, curators guide
Invalid syntax (disallowed whitespace) WARN 40 tbd
Invalid syntax (length) WARN 36 tbd

Download group

See schema docs & curators guide

labels group

Verification Log level Issue Status
url: API usage, curators guide
Invalid syntax (pattern) ERROR 34 tbd
Broken link/td> WARN 12 tbd
type: API usage, curators guide
Invalid value (must adhere to controlled vocabulary) ERROR 39 tbd
note: API usage, curators guide
Invalid syntax (disallowed whitespace) WARN 40 tbd
Invalid syntax (length) WARN 36 tbd

Documentation group

See schema docs & curators guide

labels group

Verification Log level Issue Status
url: API usage, curators guide
Invalid syntax (pattern) ERROR 34 tbd
Broken link WARN 12 tbd
type: API usage, curators guide
Invalid value (must adhere to controlled vocabulary) ERROR 39 tbd
note: API usage, curators guide
Invalid syntax (disallowed whitespace) WARN 40 tbd
Invalid syntax (length) WARN 36 tbd

Publications group

See schema docs & curators guide

labels group

Verification Log level Issue Status
General publication verifications:
Duplicate publication ID ERROR 2, 1 tbd
doi: API usage, curators guide
Invalid syntax (pattern) ERROR 34 tbd
Suspect DOI syntax (terminal fullstop) WARN 23 tbd
Unresolvable publication ID ERROR 5, 20 tbd
pmid: API usage, curators guide
Invalid syntax (pattern) ERROR 34 tbd
Unresolvable publication ID ERROR 5 tbd
pmcid: API usage, curators guide
Invalid syntax (pattern) ERROR 34 tbd
Unresolvable publication ID ERROR 5 tbd
type: API usage, curators guide
Invalid value (must adhere to controlled vocabulary) ERROR 39 tbd
version: API usage, curators guide
Invalid syntax (disallowed characters) WARN 37 tbd
Invalid syntax (length) WARN 36 tbd

Credits group

See schema docs & curators guide

labels group

Verification Log level Issue Status
General credit verifications:
Duplicate credit (of various types) ERROR 14 tbd
elixirNode: API usage, curators guide
Invalid value (must adhere to controlled vocabulary) ERROR 39 tbd
Duplicate elixirNode credit ERROR 13 tbd
elixirPlatform: API usage, curators guide
Invalid value (must adhere to controlled vocabulary) ERROR 39 tbd
Duplicate elixirPlatform credit ERROR 13 tbd
name: API usage, curators guide
Invalid syntax (disallowed characters) WARN 37 tbd
Invalid syntax (disallowed whitespace) WARN 40 tbd
Invalid syntax (length) WARN 36 tbd
email: API usage, curators guide
Invalid syntax (pattern) ERROR 34 tbd
url: API usage, curators guide
Invalid syntax (pattern) ERROR 34 tbd
Broken link WARN 12 tbd
orcidid: API usage, curators guide
Invalid syntax (pattern) ERROR 34 tbd
Unresolvable ORCID ID ERROR 45 tbd
typeEntity: API usage, curators guide
Invalid value (must adhere to controlled vocabulary) ERROR 39 tbd
typeRole: API usage, curators guide
Invalid value (must adhere to controlled vocabulary) ERROR 39 tbd
note: API usage, curators guide
Invalid syntax (disallowed whitespace) WARN 40 tbd
Invalid syntax (length) WARN 36 tbd

General verifications

Verification Log level Issue Status
tool IDs
Unverified toolID ERROR 11 tbd
duplicates
Suspected duplicate entry WARN 25 tbd
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