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BioinfoNet / OpenScienceKEHackathon

Planning for the OpenScienceKE Hackathon held on the 30th and 31st August.
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Status of open science in Kenya: Data mining #1

Open kipkurui opened 5 years ago

kipkurui commented 5 years ago

Explore the status of open science in Kenya through literature search and data mining. The idea is to analyze how open science tools have been used in research. For example, for a given period of time, we can explore how often published work in Kenya provides access to data and code. Where R has been used for data analysis, is the code provided, and through which means?

We could perform data analysis using R or Python. Tools like ContentMine could be used for this project. They have a tool for downloading papers: get papers.

Let's discuss.

kipkurui commented 5 years ago

We'll also explore using pubmed.mineR to perform text mining on Pubmed Abstracts. Used to extract these data by Geoffrey Siwo

Shuyib commented 5 years ago

This is great! I'll go through the vignette. I was intending to search for keywords associated with open science research papers i.e take a subset of a couple of papers then we cluster those as a start as well as the technologies used + text mining the content of all the papers with an app i've made + searching for trends about our keywords across the internet.

karegapauline commented 5 years ago

This is a good idea Ben.

On Wed, Aug 22, 2018 at 4:42 PM Ben Mainye notifications@github.com wrote:

This is great! I'll go through the vignette. I was intending to search for keywords associated with open science research papers i.e take a subset of a couple of papers then we cluster those as a start as well as the technologies used + text mining the content of all the papers with an app i've made + searching for trends about our keywords across the internet.

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub https://github.com/BioinfoNet/OpenScienceKEHackathon/issues/1#issuecomment-415035991, or mute the thread https://github.com/notifications/unsubscribe-auth/AaJcR390ZL9mNDKvB7shPFrTkL8uo19eks5uTV_UgaJpZM4V8CBg .

esohkevin commented 5 years ago

NCBI has also developed a tool (https://github.com/esohkevin/OpenScienceKEHackathon/blob/master/EDirect.md) that is just as robust in text mining. It can be used to access all NCBI databases

kipkurui commented 5 years ago

Awesome, thanks @esohkevin and @Shuyib. I like how this is shaping up!

ousodaniel commented 5 years ago

You got an app! awesome we definitely need to use that too even as we the others, what do you call? Some vignette?. . .

On Wed, 22 Aug 2018 at 16:42, Ben Mainye notifications@github.com wrote:

This is great! I'll go through the vignette. I was intending to search for keywords associated with open science research papers i.e take a subset of a couple of papers then we cluster those as a start as well as the technologies used + text mining the content of all the papers with an app i've made + searching for trends about our keywords across the internet.

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub https://github.com/BioinfoNet/OpenScienceKEHackathon/issues/1#issuecomment-415035991, or mute the thread https://github.com/notifications/unsubscribe-auth/AaTdxpYtqLm8rLQS6p6ISFSbnApXfJhEks5uTV_UgaJpZM4V8CBg .

-- If it only benefits me, then it is not worth it.

Ouso Daniel, BSC. Molecular & Cell Biology, P.O BOX 6547-00100. NAIROBI.

Cell:+254736865158/+254714483013 Email:ousodaniel@gmail.com

Skype: ouso.daniel

ousodaniel commented 5 years ago

Great Esoh

On Wed, 22 Aug 2018 at 18:22, Esoh Kevin notifications@github.com wrote:

NCBI has also developed a tool ( https://github.com/esohkevin/OpenScienceKEHackathon/blob/master/EDirect.md) that is just as robust in text mining. It can be used to access all NCBI databases

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub https://github.com/BioinfoNet/OpenScienceKEHackathon/issues/1#issuecomment-415071280, or mute the thread https://github.com/notifications/unsubscribe-auth/AaTdxsm7oNRKhE4J3IAymLIgCtu1TPN4ks5uTXcsgaJpZM4V8CBg .

-- If it only benefits me, then it is not worth it.

Ouso Daniel, BSC. Molecular & Cell Biology, P.O BOX 6547-00100. NAIROBI.

Cell:+254736865158/+254714483013 Email:ousodaniel@gmail.com

Skype: ouso.daniel

kmut2030 commented 5 years ago

Good work, sorry i've been away but now I'm back ...

kipkurui commented 5 years ago

Welcome Kelvin. Your presence has been missed.

mgawe-cavin commented 5 years ago

I registered with BMC-bioinformatics journal, I have been getting updates whenever any paper is published. There are a lot of codes and bioinformatics algorithms being published but majority of authors of these papers are not from kenya. A lot of R packages code can be pulled from this site (BMC-bioinformatics methods).

Shuyib commented 5 years ago

Biopython can also be used for search however, it's more inclined for searching for information about specific things for instance genes, organisms. On the other hand, i found if your searching for abstracts from your PC then it's simple. I'll just point it out.