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102 lines
2.9 KiB
XML
102 lines
2.9 KiB
XML
<tool id="hgv_funDo" name="FunDO" Version="1.0.0">
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<description>human genes associated with disease terms</description>
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<command interpreter="perl">
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disease_ontology_gene_fuzzy_selector.pl $build $out_file1 ${GALAXY_DATA_INDEX_DIR}/funDo.loc '$term'
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</command>
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<inputs>
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<param name="build" type="select" label="Database build">
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<options from_file="funDo.loc">
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<column name="name" index="0"/>
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<column name="value" index="0"/>
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<filter type="unique_value" column="0"/>
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</options>
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</param>
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<param name="term" size="40" type="text" label="Disease term(s)" />
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</inputs>
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<outputs>
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<data format="interval" name="out_file1">
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</data>
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</outputs>
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<tests>
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<test>
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<param name="term" value="lung"/>
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<param name="build" value="hg18"/>
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<output name="out_file1" file="funDo_output1.interval" />
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</test>
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</tests>
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<help>
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**Dataset formats**
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There is no input dataset. The output is in interval_ format.
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.. _interval: ./static/formatHelp.html#interval
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-----
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**What it does**
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This tool searches the disease-term field of the DOLite mappings
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used by the FunDO project and returns a set of genes that
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are associated with terms matching the specified pattern. (This is the
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reverse of what FunDO's own server does.)
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The search is case insensitive, and selects terms that contain any of
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the given words, either exactly or within a longer word (e.g. "nemia"
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selects not only "anemia", but also "hyperglycinemia", "tyrosinemias",
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and many other things). Multiple words should be separated by spaces,
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not commas. As a special case, entering the word "disease" returns all
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genes associated with any disease, even if that word does not actually
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appear in the term field.
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Website: http://django.nubic.northwestern.edu/fundo/
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-----
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**Example**
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Typing::
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carcinoma
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results in::
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1. 2. 3. 4. 5. 6. 7.
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chr11 89507465 89565427 + NAALAD2 10003 Adenocarcinoma
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chr15 50189113 50192264 - BCL2L10 10017 Carcinoma
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chr7 150535855 150555250 - ABCF2 10061 Clear cell carcinoma
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chr7 150540508 150555250 - ABCF2 10061 Clear cell carcinoma
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chr10 134925911 134940397 - ADAM8 101 Adenocarcinoma
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chr10 134925911 134940397 - ADAM8 101 Adenocarcinoma
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etc.
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where the column contents are as follows::
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1. chromosome name
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2. start position of the gene
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3. end position of the gene
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4. strand
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4. gene name
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6. Entrez Gene ID
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7. disease term
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-----
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**References**
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Du P, Feng G, Flatow J, Song J, Holko M, Kibbe WA, Lin SM. (2009)
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From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose
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ontology for the test of gene-ontology associations.
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Bioinformatics. 25(12):i63-8.
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Osborne JD, Flatow J, Holko M, Lin SM, Kibbe WA, Zhu LJ, Danila MI, Feng G, Chisholm RL. (2009)
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Annotating the human genome with Disease Ontology.
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BMC Genomics. 10 Suppl 1:S6.
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</help>
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</tool>
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