PubMed

Data from pubmed. entire file is downloaded, only taxon IDs set in project.xml will be loaded. if nothing configured, processes all entries.

Types of data loaded

genes, publications

How to download the data files

• ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2pubmed.gz
• ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz

Unzip both files, save gene2pubmed under a directory named pubmed, e.g. DATA_DIR/pubmed. It’s suggested to save gene_info in a different directory, e.g. DATA_DIR/ncbi-gene, but you can always save both in pubmed directory, see how to config below.

How to load the data into your mine

After code refactory and optimization, the current PubMed coverter will make use of id resolver to parse gene information (see how to setup Id Resolvers), whereafter the infoFile property was removed from the config.

If gene2pubmed is the only file in DATA_DIR/pubmed directory, you can remove src.data.dir.includes property, but do keep it if you place gene2pubmed and gene_info in pubmed dir at the same time.

project XML example

<source name="pubmed-gene" type="pubmed-gene">
  <property name="src.data.dir" location="DATA_DIR/pubmed/" />
  <property name="pubmed.organisms" value="7227"/>
  <property name="src.data.dir.includes" value="gene2pubmed"/>
</source>

project XML example for InterMine 1.1 and older

<source name="pubmed-gene" type="pubmed-gene">
  <property name="src.data.dir" location="DATA/pubmed/" />
  <property name="pubmed.organisms" value="7227"/>
  <property name="src.data.dir.includes" value="gene2pubmed"/>
  <property name="infoFile" location="DATA_DIR/ncbi-gene/gene_info"/>
</source>