Sentence examples for cross reference file from inspiring English sources
A list of allowed relationships are available in the go_annotation_extension_relations.obo file (http://viewvc.geneontology.org/viewvc/GO-SVN/trunk/ontology/extensions/go_annotation_extension_relations.obo) while the format for the various database identifiers can be found in the GO cross reference file (http://www.geneontology.org/doc/GO.xrf_abbs) (manuscript in preparation).
Genes defined in other databases were according to cross reference files as describe in the Methods section.
Zebrafish transcriptome cross reference files were downloaded from Ensembl (Zv7, July 2007), RefSeq (Zv7 Build3, July 2008), GenBank (October 23, 2008), Biomart (Zv7, Ensembl 52 genes) and ZFIN (October 23, 2008) (Table 1).
We downloaded the human annotation file version 60.0 and human cross-reference file version 3.39 from the GOA website http://www.ebi.ac.uk/GOA/.ac.uk/GOA/
These lists of genes were then mapped to the appropriate Swiss-Prot ID with the above mentioned GOA human cross-reference file.
Probeset IDs of each category were first mapped to NCBI Entrez gene IDs according to the Affymetrix Chicken Array annotation file, and then were mapped to KEGG gene IDs according to the KEGG gene cross-reference file.
Probeset IDs of each category were first mapped to NCBI Entrez gene IDs according to the Agilent Chicken Array annotation file, and then were mapped to KEGG gene IDs according to the KEGG gene cross-reference file.
For bioinformatics analysis, each IPI accession number was converted to an Entrez Gene ID according to the IPI protein cross-references file downloaded from http://ftp.ebi.ac.uk/pub/databases/IPI.ac.uk/pub/databases/IPI
The cross-reference files link the transcript IDs with gene IDs.
Publicly available database cross-reference files are used to look up GO association files and retrieve GO annotations for the Blast matches.
Because the different databases use different identifiers, the original identifiers were mapped to the corresponding Entrez Gene IDs using the cross-reference files from Entrez Gene, the HUGO Gene Nomenclature Committee HGNCC) [ 48] or Biomart [ 49].
