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
- Function group
- Labels group
- Links group
- Download group
- Documentation group
- Publications group
- Credits group
General verifications
Summary group
See schema docs & curators guide
| 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
| 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
| 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
| 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
| 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
| 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
| 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
| 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 |