The retrieval task deliberately focused on challenging gene normalization examples. Not surprisingly, assessment of the retrieval task, which included reviewing the top 5 10 retrieved articles for relevance to the input gene symbol, uncovered kinase assay the same issues described above with correct species identification and other normalization problems. This prompted the UAG to recommend either abandoning or reassessing the retrieval task to make it independent of the normali zation issues. Analysis of individual articles from three Inhibitors,Modulators,Libraries use cases To associate terms appearing in text with specific biolo gical entities is challenging to both biocurators and sys tems. There are cases where different genes share the same name, even within a same species, which is a ser ious problem because it affects the proper identification of the gene, and, in the end, impacts its annotation.

It also affects the retrieval of relevant documents about the gene, with the biocurator spending time discerning what articles are for which gene. The biocurator usually looks Inhibitors,Modulators,Libraries for contextual information to assist in disambigua tion, such as chromosomal location, identification of the organism bearing the gene, the mention of a synonym, and the mention of an encoded domain or its sequence length, and these same features could be used by the system to enable the user to manually select the correct unique identifier from a set of possibilities. In addition, there are multiple cases where the article introduces information for multiple genes and species, but the evi dence associating genes and species is outside the sen tence or paragraph containing AV-951 curatable information.

Sometimes Methods sections or figure legends indicate species origins via information about cDNA constructs or cell lines. In other cases the information is found in a cited reference and or acknowledgments, but there are cases where Inhibitors,Modulators,Libraries the organism source information is simply not provided. Systems should provide whatever means necessary to help the biocurator relate gene mentions to the correct species. Another challenging use case is the introduction of a new gene name. The curator is then tasked with captur ing the new gene name, species and linking it to a s case it is expected that the system could link to the organism genome database if the gene is not yet annotated in multi Inhibitors,Modulators,Libraries species gene or protein databases, such as Entrez Gene or UniProt.

With these use cases in mind, the UAG assessed the system using a set of articles that represented the selected problematic cases for curation described above, namely, gene Temsirolimus solubility name ambiguity, species ambiguity, or introduction of new gene names, with the main goal of assessing whether an interactive system could provide the necessary tools to assist in resolving these challen ging issues. These cases are described below.