ALMATextMiner is a system for extracting relevant bibliographic information related to groups of genes. The goal of the system is discovering and pinpointing the important facts related to a given group of genes but not to others. To do so, for each group of genes the system retrieves pertinent keywords, sentences, and links to relevant articles. These are then weighted such that information that is specifically relevant to each group is highlighted. This helps significantly in the functional annotation of each group of genes, and has the potential to undercover many other interesting informations (involvement in diseases, important mutations or alterations, connections with celullar processes and pathways, etc.). Even if the most obvious application of the system is in the annotation of microarray results, the analysis of any set of genes or proteins is possible. The system can therefore be used for a number of genomics and proteomics applications.








A novel system for detecting relationships between biological entities, as published in the literature. AlmaInteraction is a very valuable tool for aiding in the tedious and time-consuming task of gathering the information published in the literature. AlmaInteraction displays the knowledge associated to a gene, a protein, a pathway, etc. Some examples of possible uses of the system include:

  • Knowing the described relationships for a given entry.

  • Assesing the importance of a relationship.

  • Distinguish the type of relation (interaction, activation, repression, etc.)

  • Reconstructing pathways in base to bibliographic information.

  • Structure the knowledge according to year of study, authors, etc.

AlmaInteraction can be combined with AlmaTextMiner, producing a powerful system for biological analysis from knowledge sources.








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