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pjotrp committed Mar 1, 2014
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Expand Up @@ -8,7 +8,24 @@ Such a gene list may be used for identifying candidate genes connected to
a specific disease, but also may be used to compile a targeted
exome design for sequencing.

The inputs for Exominer are a list of Pubmed IDs with text files (PDF,
A quick example of a result for a search for pancreatic cancer genes
that were not listed in an exome design can be seen
[here](http://biobeat.org/examples/pancreatic_minus_new_design.html).

| gene | textmatch | description | context | resource | doi |
| ----- | --------- | ------------------------------------- | ------- | --- | --- |
| AKP8L | HAP95 | A kinase (PRKA) anchor protein 8-like | A cancer-associated RING finger protein, RNF43, is a ubiquitin ligase that interacts with a nuclear protein, HAP95 | Whole-exome sequencing of neoplastic cysts of the pancreas reveals recurrent mutations in components of ubiquitin-dependent pathways | doi:10.1073/pnas.1118046108 |

Here, the second column shows the fuzzy text match, the first column the
official HUGO name, the third column a description of the gene, the
fourth column the textual context in the publication, the fifth column
the title of the publication and the sixth column the DOI. The second
entry for AM is a false positive; quickly seen by checking the
context in the fourth column. This output is generated by a SPARQL
query and a lot of flexibility in combining resources and generating
output is possible. Note that this is just one example.

The inputs for Exominer consists of a list of Pubmed IDs with text files (PDF,
HTML, Word, Excel have to be exported to plain text first). Exominer
harvests gene names from these documents using a default symbol list
with aliases. Ideally, all texts would only contain HUGO symbols,
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