drugbank | User-friendly extensions of the DrugBank database

by dhimmel HTML Version: v1.0 License: No License

X-Ray Key Features Code Snippets Community Discussions(10)Vulnerabilities Install Support

kandi X-RAY | drugbank Summary

drugbank is a HTML library typically used in Utilities applications. drugbank has no bugs, it has no vulnerabilities and it has low support. You can download it from GitHub.

DrugBank is a publicly-available resource of drug information [1]. We rely on DrugBank for our project to repurpose drugs. We are conducting this project openly on ThinkLab, and this README will reference Thinklab discussions providing greater detail.

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Support

drugbank has a low active ecosystem.

It has 81 star(s) with 49 fork(s). There are 7 watchers for this library.

It had no major release in the last 12 months.

There are 1 open issues and 2 have been closed. On average issues are closed in 56 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of drugbank is v1.0

Quality

drugbank has no bugs reported.

Security

drugbank has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

License

drugbank does not have a standard license declared.

Check the repository for any license declaration and review the terms closely.

Without a license, all rights are reserved, and you cannot use the library in your applications.

Reuse

drugbank releases are available to install and integrate.

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drugbank Key Features

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drugbank Examples and Code Snippets

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Community Discussions

Trending Discussions on drugbank

Replace Drugbank IDs with Drug name

Splitting string in r while first column stays same

How to aggregate data of each year into ones of two, three, fours... years

'list' object has not attribute 'get' Python3.8 while getting info from XML

Using RDF, request for suggestions on how to model one to ORed (all) members of a set and one to ANDed (all) members of a set

Incorrect alphabetical order of column values

Alphabetical order does not work properly after adding a new factor in the dataframe to replace another

How to concatenate specific rows in python?

How to concantenate specific lines using awk?

Unstructured XML via non-tab deliminator?

QUESTION

Replace Drugbank IDs with Drug name

Asked 2021-Apr-04 at 20:50

I have a dataset of genes associated with drugs derived from DrugBank. I wish to simply translate all the drugbank IDs to drug names readable by a human. As you can see my main problem is that some genes are linked to multiple or even hundreds of drugs. the multiple Drug IDs are in the same comma-delimited "column" The R studio "match" or "merge function" only work for the first identifier in each column, thus effectively deleting the remainder in the same column "cell". I have found ways to do this manually on excel for my top candidates but it is not realistic for my dataset of 3000 genes.

Ideally, I would like to do something like "text to columns" but in rows, so every row would keep all its other values but only one of the multiple drugbank IDs in the cell, and then can just use the match function to replace them.

The drugbank vocabulary (.csv) looks like this: [DBvocabulary.csv]

DrugBank.ID Common.name

DB00001 Lepirudin

DB00002 Cetuximab

DB00003 Dornase alfa

DB00004 Denileukin diftitox

DB00005 Etanercept

DB00006 Bivalirudin

My dataset (.csv) has 15 columns but the important ones are:

[all_ph_active.csv]

Gene.Name DrugBank.ID

F8 DB09130

TCN2 DB00200

LDLR DB09270; DB11251; DB14003

ALB DB00070; DB00137; DB00159; DB00162; DB00214;

Any advice is welcome, thanks in advance!

...

ANSWER

Answered 2021-Apr-04 at 20:50

One way to do this would be to join the name column to the original dataframe.

I have provided a small example below

Source https://stackoverflow.com/questions/66935454

QUESTION

Splitting string in r while first column stays same

Asked 2020-Aug-29 at 05:29

Title might need some editing since I am not sure how to explain effectively.

here I have two columns and second column might have 3 object in same row but split by "|". I wrote a code to split them and write next line after dropping MESH: however It adds extra digit to first column. First row is not always 6 digits therefore a function I wrote is not helpful in here. Here is an example data

...

ANSWER

Answered 2020-Aug-29 at 05:15

You could remove the "MESH:" part from chem column and separate data into different rows based on "|".

Source https://stackoverflow.com/questions/63643509

QUESTION

How to aggregate data of each year into ones of two, three, fours... years

Asked 2020-Aug-12 at 02:56

Recently I'm working on the data analysis on cancer drugs using the "shiny" packages. In the third tab, I'd like to aggregate and sum the values of each year into those of a certain range of years, eg. into two years like 1984~1985, 1986~1987, ... or into five years like 1984~1988, 1989~1993,..., etc. The beginning year and the last year should be flexible, too. In that case, if I set the interval to 6 years and choose the beginning year as 1990 and the last year as 2012, the x axis of the heatplot should be presented as 1990~1995, 1996~2001, 2002~2007, 2008~2012(only five years rather than six). It's quite complicated for me and I've search for the answers yet cannot find a relatable one.

The code is as the followings. And the data is shared by the hyperlink. Thanks!

...

ANSWER

Answered 2020-Aug-12 at 02:56

The easiest way to do this is to employ the "%/%", which generates the integer after dividing the value by a specified number. And then, multiply that integer by that specified number. Here's the code:

Source https://stackoverflow.com/questions/63278411

QUESTION

'list' object has not attribute 'get' Python3.8 while getting info from XML

Asked 2020-May-21 at 19:46

So I'm trying to extract info from an XML file but I keep getting this error:

...

ANSWER

Answered 2020-May-21 at 19:46

I found the issue . Use this code to get the names of your products :

Source https://stackoverflow.com/questions/61933019

QUESTION

Using RDF, request for suggestions on how to model one to ORed (all) members of a set and one to ANDed (all) members of a set

Asked 2019-Jun-08 at 08:29

I am looking for a way to model using RDF a one to ORed (all) members of a set relationship as well as a one to ANDed (all) members of a set.

The task at hand how to represent (using RDF statement triples) a treatment regimen such as the one below.

Regimen "Regimen_A" consists of drug (DB14502 OR DB09449) AND DB11094

Using RDF/XML, I am now stuck at presenting the drug combination (regimen) consisting of one-of (alternative) drug from list A plus all the (non-optional) drugs from list B.

a) It is possible for a drug regimen to have zero, one or more than one alternative list as well as zero, one or more one non-optional drug list.
b) I would also like to present each drug as a resource having URIref. c) The drugs in these lists (the ORed list and the ANDed list) can be from different databases such as drugbank, ChEBI or WHOCC. For example the URIref for drugbank drug DB14502 would be "https://www.drugbank.ca/drugs/DB14502". The URI for ChEBI drug would be "http://purl.obolibrary.org/obo/CHEBI_17012" In addition to the URIref, there is a requirement to somehow explicitly provide an indication of the drug's source database.

I have been reading the RDF primer https://www.w3.org/TR/rdf-primer/ with the aim of encoding into RDF/XML the solution below as well as extend it to address the above requirements but I have not made much progress in this area.

Below is the RDF data (provided by Jeen Broekstra as an answer to my original question) I would like to transform to RDF/XML

...

ANSWER

Answered 2019-May-30 at 00:26

You can express it by introducing your own vocabulary concept for an OR.

Source https://stackoverflow.com/questions/56354727

QUESTION

Incorrect alphabetical order of column values

Asked 2019-May-23 at 06:14

I have the dataframe below:

...

ANSWER

Answered 2019-May-23 at 06:14

As mentioned in the comment, the problem is that the columns in your data frame are not characters but factors. Most of the time, it is more convenient to work with characters. In this case you can use stringsAsFactors = FALSE inside data.frame(...). Then you can order with respect to the second column:

Source https://stackoverflow.com/questions/56263561

QUESTION

Alphabetical order does not work properly after adding a new factor in the dataframe to replace another

Asked 2019-May-17 at 23:09

I have the dataframe below:

...

ANSWER

Answered 2019-May-17 at 23:09

For levels: It seems to me to be OK here. But, in case you do not get it to elucidate this, I suggest using the forcats package

Source https://stackoverflow.com/questions/56194398

QUESTION

How to concatenate specific rows in python?

Asked 2019-Feb-18 at 11:52

I am looking to learn how to concatenate multiple columns in python. I have a dataset which looks like this:

...

ANSWER

Answered 2019-Feb-18 at 11:52

Using pd.DataFrame.groupby and its agg:

Source https://stackoverflow.com/questions/54746263

QUESTION

How to concantenate specific lines using awk?

Asked 2019-Feb-15 at 12:03

I am looking to learn how to concatenate multiple columns in linux. I have a dataset which looks like this:

...

ANSWER

Answered 2019-Feb-15 at 12:03

If you are not worried about spacing part of headers then please try following.

Source https://stackoverflow.com/questions/54707385

QUESTION

Unstructured XML via non-tab deliminator?

Asked 2018-May-24 at 12:43

We have a complex XML Structure and really a big one (>500 MB). the XSD of the structure is: This XSD

As we know this is a complex one. and because of size or non-tab deliminator structure, I couldn't convert it to a readable better presentation.

I want to read this file via C# and search the drug name. what is wrong via my code?

...

ANSWER

Answered 2018-May-04 at 12:21

The simplest approach here would be to use xsd your.xsd /c, add the generated your.cs to the project, and just use XmlSerializer against whatever type is the "root" type; it looks like this will be drugbanktype, so:

Source https://stackoverflow.com/questions/50173567

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Vulnerabilities

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Install drugbank

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