mirPub Help

1. What is mirPub?

mirPub is a database and a Web application, on top, which provides a powerful and intuitive interface to researchers and database curators for searching publications related to microRNA molecules. It provides the most complete set of microRNA related publications (more than 5900 distinct papers and more than 57300 microRNA-to-publication associations). To achieve this, it considers microRNA name variations and microRNA name evolution, and it utilizes both manually curated data and text mining techniques.

2. Who are we?

mirPub is the result of the combined work of the DIANA LAB of Flemming RC and the DIWIS group of IMIS institute (Athena RC). For more information, please visit the contact section of our website.

3. How to search for publications?

The user can search for publications related to particular microRNAs by inserting keywords describing these microRNAs in the searchbox of the mirPub interface. mirPub identifies these user keywords by mapping them to a set of known microRNA keywords (these are microRNA names or variants of them). If there is any user keyword that cannot be mapped to any known microRNA keyword, then mirPub finds the most similar to it known microRNA keywords and suggests them to the user. Moreover, if a user keyword can be mapped to more than one known microRNA keywords, then mirPub presents all the available options to the user and prompts him to select which of them to include into his search query. In any other case, mirPub produces the list of publications that are found to be relevant to the identified keywords.

4. Can I search by family name?

Yes! In this case, mirPub will produce a list of all the members of this family giving you the opportunity to select only those that you are interested in.

5. Too many results! What to do?

As mirPub performs expansion of your query, it may produce some results related to keywords that are irrelevant to your search. However, all the microRNA keywords used to produce the results are displayed as hyperlinks in the “used keywords” box at the right of the result list. Thus, you can select to keep only the results related to the keywords of your interest simply by clicking one time on the corresponding hyperlinks.

6. Limited number of results! What to do?

You can search by omitting the species prefix in the microRNA name, or by searching by the family of the microRNA of your interest.

7. How to find out why a keyword is used?

The used microRNA keywords are organized in categories, and those that correspond to a mature or a hairpin are followed by an information button. After clicking on this button, a pop-up displaying the history of the related to this keyword microRNAs is rendered, to help the user to understand the reason why this keyword is used (for instance, a keyword could be an old name of the microRNA of interest).

8. Where do we get our data?

mirPub provides microRNA-to-publication associations based on the following sources:

Text mining on MEDLINE/PubMed. Correlations are mined by using predefined rules on the titles and abstracts of the papers contained in 2012 MEDLINE/PubMed baseline files. Special care is taken in order to consider microRNA evolution and microRNA name variations.
Text mining on PMC open access papers. Correlations are mined by using predefined rules on the titles and abstracts of the papers contained in PMC open access archive. Special care is taken in order to consider microRNA evolution and microRNA name variations.
Manually curated databases. Associations are collected from miRBase, Tarbase v.6.0, and mir2disease
User generated data. mirPub provides to its users the opportunity to contribute to its content by reporting problematic records or by suggesting microRNA-to-publication associations that don’t exist in its database yet.

9. There is a wrong entry! What can I do?

You can click on the “thumbs down” button located in the expanded view of each result. This action results in rendering a new page containing a form that collects some information about your request. Note, that the uploaded data become part of mirPub’s database only after moderation performed by an expert curator. This final step is required in order to keep a high level of data quality.

10. I know about a publication which is missing. What can I do?

You can click on the “Submit new results” button located below the search box. Same as with wrong entry, this action also results in rendering a new page containing a form that collects more information about your request.

11. How to suggest desired features or report bugs?

You can send an email to diana_admin@imis.athena-innovation.gr or visit the contact section of our website.

12. Where to find more information?

You can send an email to diana_admin@imis.athena-innovation.gr or visit the contact section of our website.