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How to query the synonyms database

Query interface:

Enter name to find synonyms for:

The user can enter a gene/protein name or any string of characters in the query form. The search is case-insensitive, meaning upper and lower case will be ignored. In addition the wildcard characters "*" (star) for matching arbitrary substrings and "?" (question mark) for matching any single character can be used at the end of the string.

Restrict search (optional):

  • To one species name (scientific name or common name):
  • To one/several model organisms:
  • To a taxonomic node:
  • To one/several source databases:
  • By type: limit the results to names marked as preferred gene names, or gene names, or protein names:

Start search:

After the query has been formulated, clicking the "Search" button (left bottom of the page) will submit the query, run the search and display the results.

Result interface:

Examine results:

The number of distinct synonyms and the number of entity is mentioned at the top of the page.

For each synonym listed, the source database is mentioned (under 'Source' column) with a direct link to the corresponding database entry

The result shows one synonym per row. Synonyms are grouped by species and gene/protein entity in case of homonymy. Several groups from the same species are indicative of possible homonyms (the query term is used to name different biological entities).

PubMed Query:

Select names to be queried for in PubMed:

Each group (entity) has a group header that shows the species name and a +/- selector that will select or de-select all the synonyms within this group.

From the list of synonyms, the user can also pick individual names by checking the corresponding checkboxes

The user can select or deselect all the synonyms by clicking on Select All/Select None links at the bottom page.

Get statistics

Once the synonyms are selected, the user can click the "Statistics" link to obtain numbers of PubMed publications retrieved with those synonyms.

Start PubMed search:

Once the synonyms are selected, the user click the "Query PubMed" link (bottom of the page) to query the literature database.