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pjotrp committed Mar 1, 2014
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Expand Up @@ -8,9 +8,7 @@ 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.

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).
A quick example

| gene | textmatch | description | context | resource | doi |
| ----- | --------- | ------------------------------------- | ------- | --- | --- |
Expand All @@ -19,11 +17,16 @@ that were not listed in an exome design can be seen
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 title of the publication and the sixth column the DOI.

A complete 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).
In this table the second entry for AM is a false positive; quickly
seen by checking the context in the fourth column (AM refers to author
initials). 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
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