Agilent Literature Search comes with a set of species-specific concept lexicon files, which are specified in the concept-lexicon-map.txt, in the <user.home>/.cytoscape/<Cytoscape-version>/plugins/ <AgilentLiteratureSearch-version>/data folder, which we will refer to from now on as the home folder. The concept-lexicon-map.txt file is used to identify potential "concepts" (e.g., genes, proteins, diseases, drugs, compounds, etc.). It contains a TAB-delimited list of two columns where each row represents one lexicon mapping. The first column is the name of the concept lexicon and represents the name displayed within the dropdown menu for Concept Lexicon: in the Agilent Literature Search UI. The second column is the file path, relative to the home folder, that defines this lexicon. Species specific files are currently named '.uc-<species-name>', for example '.uc_Homo_sapiens'. These concept lexicon files are located under the home folder . You can edit these files to add, modify, or delete user context terms.
The set of concept lexicon files provided with this version of Agilent Literature Search is:
.uc_Arabidopsis_thaliana
.uc_Bos_taurus
.uc_Caenorhabditis_elegans
.uc_Danio_rerio
.uc_Drosophila_melanogaster
.uc_Escherichia_coli
.uc_Homo_sapiens
.uc_Mus_musculus
.uc_Rattus_norvegicus
.uc_Saccharomyces_cerevisiae
The format of the .concept lexicon files is as follows: each line contains the formal name for the term followed by a list of aliases. All terms on every line are tab-separated. Only the formal name for the term is displayed in Cytoscape networks.
An excerpt from a uc_Homo_sapiens file is shown below: