SENT: Semantic Features in Text


1. Dataset


Description:


3. Factors

Suggestion:


4. Optional


2. Genes

See the Supported Ids. Or Translate your gene synonyms.



Precomputed Examples:

Homo sapiens:
Standard or Fine Grained . Load data
Saccharomyces cerevisiae:
Standard or Fine Grained . Load data


If you find SENT useful, please cite this publication:

Vazquez, M. and Carmona-Saez, P. and Nogales-Cadenas, R. and Chagoyen, M. and Tirado, F. and Carazo, J.M. and Pascual-Montano, A.: SENT: semantic features in text. Nucleic Acids Research 2009, doi:10.1093/nar/gkp392 [Pubmed]

Fine grain analysis


This analysis renders results with more specific terms than the standard analysis but takes considerably longer, around 15 or 30 minutes.

Number of Factors.


Select the number of factors to produce.

You may specify a coma separated list of values to explore, ranges are also allowed. There must be a maximum of 8 different values, between 2 and 32. Example: 2-5, 10, 15. Results for each value will be showed as they are made available.

Gene Ids


Paste the gene ids.

They must be in one of the acceptable formats listed in the Supported Ids table. If gene names are available instead of gene identifiers, try the Translation tool. Ids may be separated by comas or line breaks. If a file is specified it must follow this same format, and it will be used instead of the contents of the text area.

NOTE: Some ids may not be recognized, or may refer to genes with no associated articles in the system

File with gene ids


You may specify the gene ids by uploading a file instead of using the text area. If a file is specified the ids in the text area will be ignored

Literature Index


Building the literature index will enable the literature examination, which presents the articles used in the analysis sorted according to the relevance to each particular semantic feature.

Dataset Selection


Select the organism the genes belong to.

If 'Custom Associations' is selected, you will be asked to provide a text file with the associations. One association per line, listing the entity and a coma separated list of PubMed ids, separated by a tab character. There associations for a particular entity may also be spread out across different lines.

Associations File


Provide a text file with the associations.

One association per line, listing the entity and a coma separated list of PubMed ids, separated by a tab character. There associations for a particular entity may also be spread out across different lines.