Details
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Type: New Feature
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Status: Open
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Priority: Critical
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Resolution: Unresolved
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Affects Version/s: None
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Component/s: data retrieval services, Datamodel, file format issue, sequencefeatures
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Labels:
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Epic Link:
Description
Database cross references, including mappings between parts of the associated sequence and some other coordinate system are generated for sequences retrieved from or validated against sequence databases or other web services.
Exporting and importing sequence annotation from these sequences should allow database cross-reference information to be exchanged, but currently, no standard types have been defined for recording database cross references or for implementing them.
1. Define/research common types used for recording database cross references (dbref, dbxref, db_ref are typical and part of biosapiens/sequence ontology).
2. specify model for annotating a cross reference with information about how the local sequence maps to the external source (e.g. PDB residue numbers for positions in a uniprot sequence).
3. create tests to ensure that newly validated sequences and sequences with database cross references stored in jalview projects can be exported as flat files and reimported.
Exporting and importing sequence annotation from these sequences should allow database cross-reference information to be exchanged, but currently, no standard types have been defined for recording database cross references or for implementing them.
1. Define/research common types used for recording database cross references (dbref, dbxref, db_ref are typical and part of biosapiens/sequence ontology).
2. specify model for annotating a cross reference with information about how the local sequence maps to the external source (e.g. PDB residue numbers for positions in a uniprot sequence).
3. create tests to ensure that newly validated sequences and sequences with database cross references stored in jalview projects can be exported as flat files and reimported.
Attachments
Issue Links
- related with
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JAL-1089 jalview features with html descriptions containing URL links with bare '&' (ampersands) incorrectly parsed
- Open
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JAL-1088 non-fetchable database references displayed in the 'get crossreferences submenu'
- Open
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JAL-487 use picr to resolve id cross references
- Open
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JAL-906 use obo ontologies for collecting data and analysis services into categories
- Open