How To Retrieve The Data From A Web Database

Question

[AP]

Hi,

am planning to develop an application to filter an article of a scientific journal based on keyword search and extract the data from a website. i have no clue how should i go about. Please anyone can provide me with more information.

[Pierre Lindenbaum]

what is the "data" ?

[Sean Davis]

What website are you querying?

[Alex Paciorkowski]

Yes, to help you, we require these details...

[Neilfws]

If you really have "no clue", you probably need to learn the basic skills required before even trying to develop an application. Most people have at least "some clue" before they start. BioStar provides answers to questions, not educational training.

[AP]

sorry for not giving more information. i want to look up for a drug names in a article and using keyword search and once the names are found the further information of that drug has to obtained from kegg drug database. how would i start with the workflow for this.

Answer 1

[Michael]

I suggest to start reading all you can get about text-mining, more specifically possibly mining pubmed articles. We have had related posts here but in the meantime I have learned to understand that, if beginning from scratch, it can be difficult to even know the right terms to search for in google.

I could be a good start to simply go through all questions on Biostar on text mining: http://www.biostars.org/search/?q=text-mining (72 hits). Then you can possibly better define your goals and set priorities. You need to have a certain amount of basic knowledge about the topic to be able to define your project correctly, and it is certainly helping to look at what others are working with.

Likely a good start:

• http://www.biostars.org/post/show/48265/text-mining-clinicaltrialsgov-for-drug-gene-interactions/#48280
• http://www.biostars.org/post/show/12326/examples-of-full-text-mining-on-the-pubmed-central-open-access-subset/

[AP]

That was useful. Actually am looking for an algorithm like KEA for keyword extraction. Are there anymore algorithm?

Answer 2

[Sean Davis]

For searching pubmed, you'll want to read and understand about eUtils. I'm not clear on what you are trying to do other than to find information about drugs, but pubmed searching sounds like it will be part of the workflow.