Does someone know a literature search algorithm?

Question

[Avro]

Hi everyone,

I keep hearing about algorithms to search the literature for gene associations. For example, I have a gene list, and I would like to search the literature for gene associations with each of the gene in my list. I could do it manually, but it seems that search algorithms would be more effective. For example, once I fish out a new gene association, I could simply read the respective paper for more details. There is LitVAn from Pe'er's lab, but I can't access it on their website.

I would greatly appreciate if someone could suggest another search algorithm.

Thank you for your time.

[Ashutosh Pandey]

Try Chilibot (Chilibot searches PubMed literature database (abstracts) about specific relationships between proteins, genes, or keywords.)

[Dan D]

I'd never heard of Chilibot. That looks incredibly useful.

[Avro]

Hi! Thank you! I am reading the paper. I was wondering: although it's 10 years old, is it still one of the best algorithm? It seems very good!

[Avro]

I forgot to ask you: according to the webpage, Chilibot is no longer available for download, but the "synonym database used in Chilibot is available." What does it mean? Thank you!

[Ashutosh Pandey]

Genes have aliases. So if you give a gene name as an input then chilibot will automatically expand the query to its aliases. The synonym database refers to list of genes with their aliases.

[Ashutosh Pandey]

Here is another tool. It uses both the experimental datasets and literature to find the connections.

[Ram]

Maybe just search "gene association" AND <gene-name> on Pubmed? What is your manual search algorithm, as in how do you do it manually right now?

Answer 1

[Dan D]

I'm not sure which programming language you want to use, but here's a very helpful general overview of how to programmatically search Entrez resources (such as PubMed) and handle the results from generated queries. If you provide more specifics I can probably help you out further. Comment on this answer and I'll update it accordingly.

[Avro]

Hi Deedee! Thank you for your time. I am reading the documentation. Is it ok if I ask questions later?

[Dan D]

Of course! Ask whatever, whenever.