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.
1 answer
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.
Log in to answer this question.
-
Is there a way to find the GWAS traits to a gene programmatically?
written by cmcouto.silva •
-
Text mining in PDFs
written by Matt LaFave
-
A comparison of 'Closest-neighbour-interchange' and 'Nearest-neighbour-interchnage' algorithms
written by mdsiddra •
-
Tool: Open Targets batch search, your list of human genes matched to our disease associations
written by Denise CS
-
Basic idea of applying a gene signature
written by Avro
-
Naive Bayes classifier for identification of human tumors
written by Avro
-
How to convert Illumina probe expression data into gene expression data?
written by Avro
-
Is there a method as good/superior as GISTIC/JISTIC to detect cancer-driving copy number alteration…
written by Avro
-
Estimate transcription factors binding sites for Drosophila genes
written by EvoGen •
-
Gpu Accelerated Tool For Wrapper Feature Selection In Microarray Classification
written by mattia.bosio85 •
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?
Try Chilibot (Chilibot searches PubMed literature database (abstracts) about specific relationships between proteins, genes, or keywords.)
I'd never heard of Chilibot. That looks incredibly useful.
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!
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!
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.
Here is another tool. It uses both the experimental datasets and literature to find the connections.