Figure 4.

Pathway construction flowchart. The initial step consists of a PubMed search with the subject of interest (e.g. preimplantation development). The list of PubMed identifiers (PMIDs) obtained in the search is then used in the web tool Medline Ranker as the background set along with a list of PMIDs of manually selected abstracts considered informative which form the test set. The tool generates a list of abstracts classified by order of relevance. Best 1000 abstracts are recovered and their corresponding PMID is then introduced in the PESCADOR platform. Abstracts are tagged by PESCADOR and provide a source of biointeractions for manual curation and pathway construction. UniProt IDs for products of the genes present in the final pathway are obtained and used as seed in SeedServer. The software recruits homologues for each gene and creates the final clusters. Taxonomy IDs from each cluster can be used for Last Common Ancestor (LCA) determination.

Donnard et al. BMC Genomics 2011 12(Suppl 4):S3   doi:10.1186/1471-2164-12-S4-S3