Commit 8e6a7f70 authored by lmueller's avatar lmueller
Browse files

added taxonomy to documentation

parent d60fa151
......@@ -14,6 +14,7 @@ Welcome to DBXRef resolve and retrieval tool's documentation!
gene_ontology
pfam
sequence_ontology
taxonomy
uniprot
......
.. highlight:: yaml
Taxonomy
=============
Retrieve gene ontology documents for dbxrefs and convert them into json.
Options
-------
* ``--basic`` - include id, scientificName, commonName, lineage and rank
* ``--geneticCodes`` - include id, geneticCode and mitochondrialGeneticCode
Input
-----
example: ``Taxon:7227``
Output
------
output scheme::
default output:
[
{
"commonName": "common name of the Taxon",
"geneticCodes": {
"geneticCode": "genetic code of the Taxon",
"mitochondrialGeneticCode": "mitochondrial genetic code of the Taxon"
},
"id": "dbxref of the Taxon",
"lineage": "lineage of the Taxon",
"rank": "rank of the Taxon",
"scientificName": "scientific name of the Taxon"
}
]
--basic output:
[
{
"commonName": "common name of the Taxon",
"id": "dbxref of the Taxon",
"lineage": "lineage of the Taxon",
"rank": "rank of the Taxon",
"scientificName": "scientific name of the Taxon"
}
]
--geneticCodes output:
[
{
"geneticCodes": {
"geneticCode": "genetic code of the Taxon",
"mitochondrialGeneticCode": "mitochondrial genetic code of the Taxon"
},
"id": "dbxref of the Taxon"
}
]
example output::
[
{
"commonName" : "fruit fly",
"geneticCodes" : {
"geneticCode" : "1",
"mitochondrialGeneticCode" : "5"
},
"id" : "Taxon:7227",
"lineage" : "Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Holometabola; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila; Sophophora; ",
"rank" : "species",
"scientificName" : "Drosophila melanogaster"
}
]
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