bioagentsLint is under design : coding has not started and this page may be missing information
bioagentsLint is a utility for verification and reporting of content of the IECHOR Agents & Data Services Registry. It will, for purposes of content quality control and labelling, verify the content according to:
- agent description syntax defined by [bioagents schema](https://github.com/bio-agents/bioagents schema)
- correct or recommended use of the EDAM ontology
- curation best practice from the bio.agents Curators Guide (in so far as these recommendations can be automatically verified)
- compliance to the Agent Information Standard
- miscellaneous other checks, e.g. broken link detection, agent name uniqueness etc.
The verifications are exhaustively tabulated below, including one table / element group defined in bioagents schema.
- Summary group
- Function group
- Labels group
- Links group
- Download group
- Documentation group
- Publications group
- Credits 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.agents) | 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 agent 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 agent homepage URL | WARN | 38 | tbd |
| bioagentsID: API usage, curators guide | |||
| Mismatch of bioagentsID & bioagentsCURIE | WARN | 22 | tbd |
| bioagentsCURIE: API usage, curators guide | |||
| Mismatch of bioagentsID & bioagentsCURIE | 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 |
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.
See schema docs & curators guide
| Verification | Log level | Issue | Status |
| agentType: API usage, curators guide | |||
| Invalid value (must adhere to controlled vocabulary) | ERROR | 39 | tbd |
| Duplicated agentType | 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 |
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 |
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 |
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 |
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 |
See schema docs & curators guide
| Verification | Log level | Issue | Status |
| General credit verifications: | |||
| Duplicate credit (of various types) | ERROR | 14 | tbd |
| iechorNode: API usage, curators guide | |||
| Invalid value (must adhere to controlled vocabulary) | ERROR | 39 | tbd |
| Duplicate iechorNode credit | ERROR | 13 | tbd |
| iechorPlatform: API usage, curators guide | |||
| Invalid value (must adhere to controlled vocabulary) | ERROR | 39 | tbd |
| Duplicate iechorPlatform 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 |
| Verification | Log level | Issue | Status |
| agent IDs | |||
| Unverified agentID | ERROR | 11 | tbd |
| duplicates | |||
| Suspected duplicate entry | WARN | 25 | tbd |