FAQ

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Gus Hahn-Powell edited this page Oct 13, 2016 · 8 revisions

What do I need to compile and run Reach from source?

Java 8
sbt (any version will do, as the proper version will be retrieved at compile time)
At least 5G of RAM (see the .sbtopts file)

What formats can Reach read?

You can find a description our supported input formats here: https://github.com/clulab/reach/wiki/Supported-Input-Formats

How can I download an `nxml` file from the OpenAccess subset of PubMed?

Here are two solutions:

Use a url of this format: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=<pmc id sans pmc goes here>&retmode=xml

If we wanted to retrieve PMC26816343, this would be the formatted url:
- http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=26816343&retmode=xml

You can run this Python (2.7 or 3.x) script: https://gist.github.com/myedibleenso/f233359445461a71ad37017393fe921f