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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_path}/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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