jakelever/cancermine

Text-mined knowledgebase for drivers, oncogenes and tumor suppressors in cancer

cancermine's Issues

cancermine

cancermin 的依赖版本能提供一下吗 ，犹豫spacy的版本问题导致一系列依赖混乱

Minor issue - antisense (AS1) occurrences

Hi Jake,

Lately, I discovered a minor issue with some of the hits. As it happens, a lot of protein-coding genes also have an antisense transcript, and it seems as if these occurrences in the literature are catched along with the primary (protein-coding) genes. Basically, you will see occurrences of <gene_symbol>-AS1 in addition to <gene_symbol>, which are currently both normalized to gene_symbol, but ideally I think they should probably be considered separate entities? I have set up a simple post-filter scheme to catch them, but if you are not aware I thought it might be of interest.

kind regards,
Sigve

Cannot download data

Hi @jakelever ,

I am trying to download different types of genes based on cancer type for medulloblastoma from http://bionlp.bcgsc.ca/cancermine/. But when I want to download the table it says "download failed".
Do you know what is wrong?

Thanks,
Vahid.

Minor issue - TTN as oncogene

Hi @jakelever,

Just discovered what I believe to be an artefact from the latest release, indicating quite some support for TTN as an oncogene. Having looked at the sentences in the supporting citations (using http://bionlp.bcgsc.ca/cancermine/), it seems that TTN is mistakenly (?) tagged in the context of a non-coding RNA with a name that includes TTN (TTN-AS1). Given that TTN is one of the largest protein-coding genes, mutations in this gene are very frequent in human tumors (purely by chance due to its large size), but quite sure this is not an oncogene.

Just thought it might be relevant for check/improvements of your text mining pipeline.

kind regards,
Sigve

Data update v29 - increase in unfiltered and drop in sentences

Hi,

Quick question regarding data update October 2020. I notice a dramatic increase in the size of cancermine_unfiltered.tsv, and a drop in the cancermine_collated.tsv, not following the trends in previous releases. Is this as expected?

kind regards,
Sigve

Error in accessing the web portal

Hi, thank you for your effort in constructing a database for the cancer driver genes.
I have a question about the web portal.
When I tried to use the database from https://bionlp.bcgsc.ca/cancermine/ , I couldn't access to the site with the error.

The following error was encountered while trying to retrieve the URL: https://bionlp.bcgsc.ca/cancermine/

This request could not be forwarded to the origin server or to any parent caches.

Some possible problems are:

An Internet connection needed to access this domains origin servers may be down.
All configured parent caches may be currently unreachable.
The administrator may not allow this cache to make direct connections to origin servers.
Your cache administrator is root.

Can you check it?