[2] | 1 | <tool id="hgv_funDo" name="FunDO" Version="1.0.0"> |
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| 2 | <description>human genes associated with disease terms</description> |
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| 3 | |
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| 4 | <command interpreter="perl"> |
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| 5 | disease_ontology_gene_fuzzy_selector.pl $build $out_file1 ${GALAXY_DATA_INDEX_DIR}/funDo.loc '$term' |
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| 6 | </command> |
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| 7 | |
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| 8 | <inputs> |
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| 9 | <param name="build" type="select" label="Database build"> |
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| 10 | <options from_file="funDo.loc"> |
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| 11 | <column name="name" index="0"/> |
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| 12 | <column name="value" index="0"/> |
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| 13 | <filter type="unique_value" column="0"/> |
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| 14 | </options> |
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| 15 | </param> |
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| 16 | <param name="term" size="40" type="text" label="Disease term(s)" /> |
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| 17 | </inputs> |
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| 18 | |
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| 19 | <outputs> |
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| 20 | <data format="interval" name="out_file1"> |
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| 21 | </data> |
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| 22 | </outputs> |
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| 23 | |
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| 24 | <tests> |
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| 25 | <test> |
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| 26 | <param name="term" value="lung"/> |
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| 27 | <param name="build" value="hg18"/> |
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| 28 | <output name="out_file1" file="funDo_output1.interval" /> |
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| 29 | </test> |
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| 30 | </tests> |
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| 31 | |
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| 32 | <help> |
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| 33 | **Dataset formats** |
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| 34 | |
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| 35 | There is no input dataset. The output is in interval_ format. |
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| 36 | |
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| 37 | .. _interval: ./static/formatHelp.html#interval |
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| 38 | |
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| 39 | ----- |
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| 40 | |
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| 41 | **What it does** |
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| 42 | |
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| 43 | This tool searches the disease-term field of the DOLite mappings |
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| 44 | used by the FunDO project and returns a set of genes that |
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| 45 | are associated with terms matching the specified pattern. (This is the |
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| 46 | reverse of what FunDO's own server does.) |
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| 47 | |
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| 48 | The search is case insensitive, and selects terms that contain any of |
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| 49 | the given words, either exactly or within a longer word (e.g. "nemia" |
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| 50 | selects not only "anemia", but also "hyperglycinemia", "tyrosinemias", |
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| 51 | and many other things). Multiple words should be separated by spaces, |
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| 52 | not commas. As a special case, entering the word "disease" returns all |
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| 53 | genes associated with any disease, even if that word does not actually |
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| 54 | appear in the term field. |
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| 55 | |
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| 56 | Website: http://django.nubic.northwestern.edu/fundo/ |
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| 57 | |
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| 58 | ----- |
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| 59 | |
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| 60 | **Example** |
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| 61 | |
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| 62 | Typing:: |
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| 63 | |
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| 64 | carcinoma |
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| 65 | |
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| 66 | results in:: |
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| 67 | |
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| 68 | 1. 2. 3. 4. 5. 6. 7. |
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| 69 | chr11 89507465 89565427 + NAALAD2 10003 Adenocarcinoma |
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| 70 | chr15 50189113 50192264 - BCL2L10 10017 Carcinoma |
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| 71 | chr7 150535855 150555250 - ABCF2 10061 Clear cell carcinoma |
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| 72 | chr7 150540508 150555250 - ABCF2 10061 Clear cell carcinoma |
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| 73 | chr10 134925911 134940397 - ADAM8 101 Adenocarcinoma |
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| 74 | chr10 134925911 134940397 - ADAM8 101 Adenocarcinoma |
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| 75 | etc. |
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| 76 | |
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| 77 | where the column contents are as follows:: |
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| 78 | |
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| 79 | 1. chromosome name |
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| 80 | 2. start position of the gene |
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| 81 | 3. end position of the gene |
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| 82 | 4. strand |
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| 83 | 4. gene name |
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| 84 | 6. Entrez Gene ID |
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| 85 | 7. disease term |
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| 86 | |
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| 87 | ----- |
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| 88 | |
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| 89 | **References** |
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| 90 | |
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| 91 | Du P, Feng G, Flatow J, Song J, Holko M, Kibbe WA, Lin SM. (2009) |
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| 92 | From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose |
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| 93 | ontology for the test of gene-ontology associations. |
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| 94 | Bioinformatics. 25(12):i63-8. |
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| 95 | |
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| 96 | Osborne JD, Flatow J, Holko M, Lin SM, Kibbe WA, Zhu LJ, Danila MI, Feng G, Chisholm RL. (2009) |
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| 97 | Annotating the human genome with Disease Ontology. |
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| 98 | BMC Genomics. 10 Suppl 1:S6. |
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| 99 | |
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| 100 | </help> |
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| 101 | </tool> |
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