Bioinformatics Project from Scratch - Drug Discovery Part 1 (Data Collection and Pre-Processing)

[@DataProfessor]

👉Watch this video next (How to learn data science in 2021) kzbin.info/www/bejne/pYOZaGOKrdybbpo Support this Channel 👇👇👇 🌟 Buy me a coffee www.buymeacoffee.com/dataprofessor 🌟 Download Kite for FREE www.kite.com/get-kite/? 👉 Subscribe to this KZbin channel kzbin.info 👉 Join the Newsletter of Data Professor newsletter.dataprofessor.org 👉 Blogs on Medium medium.dataprofessor.org/

[@aadimnepal6497]

Hi Professor. Where can I find the documentation for CHEMBL library?

[@kapilkumar-jn4il]

Dear sir, Indian card does not support automatics payment please set for a prepaid plan. I am getting into trouble paying.

[@suthishmababu2107]

Do you have documentation for this project

[@soukisama05]

Dear Data Professor, I can not even express how grateful I am for your content and dedication to your subscribers! I come from a biological background and I am new to the bioinformatic world. You give me motivation and great advice to continue studying in this incredible field. Great work, Greetings from Brazil!

[@DataProfessor]

Wow, thank you! Glad the contents are helpful to your journey into bioinformatics 😃

[@DataProfessor]

Thanks to the discussion with Shweta in this comment section. Back in the days, 7 years ago, we manually compiled the bioactivity data of more than 2000 compounds from hundreds of research articles. The whole process took 6 months, then we spent a few more months manually curating the data, and double checking again and again for consistency. Fast forward to today, we can do the same thing in less than 10 minutes as shown in this video. I am thankful for the generosity of data providers for making these APIs as well as the various libraries such as pandas (imagine handling hundreds of Excel files and manually curating those) and scikit-learn (imagine optimizing learning parameters manually on 50 computers and via a GUI interface of data mining software such as Weka). Coding is indeed a real superpower. If you are thinking of whether to learn coding or not, my recommendation is yes! It will be one of the best decision for your career and hobby 😃

[@shwetaredkar734]

Very true. I thank you on behalf of all your subscribers for all the efforts and getting such super amazing tutorials to all of us.

[@DataProfessor]

@@shwetaredkar734 I'm flattered.Thanks for the kind words. Glad the tutorials were helpful.

[@kapilkumar-jn4il]

@@DataProfessor need help sir

[@khaifea8829]

As a Bioinformatics MSc student I found this so interesting

[@DataProfessor]

Thanks Muhammad for watching and the kind comment! I am currently editing the video of Part 0 (Bioinformatics 101) and Part 2 will be filmed soon.😃

[@عمرسالمسرية2018]

hi everyone please , can anyone tell me how to get past master thesis in Bioinformatics about Drug Discovery ?

[@tiamat1628]

Brilliant sfuff thank you very much for sharing your knowledge and wisdom

[@KenJee_ds]

Can't wait for part 2! I know your subscribers have been asking for this series!

[@DataProfessor]

Thanks Ken! Inspired by subscribers and by Ken Jee’s Data Science from Scratch Series 😃

[@KenJee_ds]

@@DataProfessor haha I am flattered! Keep up the great work!

[@queenofunderland]

Me too. Yaay, thx for the video, Prof. Learned sth from my bioinformatics study, but definitely you give me more experience!

[@CostanzoPadovano]

Perfect lesson, thank you Professor! Greetings from Italy!

[@DataProfessor]

Thanks for watching and glad it is helpful 😊

[@shwetaredkar734]

This video is a treasure that I have found. Probably the first video ever on Chembl data collection. I wish this video was out when my paper was under review last year. Luckily, I could solve the reviewer query on Chembl.

[@DataProfessor]

Shweta, Thanks for the kind words! I’m flattered, glad it was helpful! 😃

[@shwetaredkar734]

@@DataProfessor seriously, I faced a lot many issues to solve the comment. May be I was not familiar with Chembl. But surely, this video will help many of them. Thanks for making this.

[@DataProfessor]

@@shwetaredkar734 Thanks for sharing. And thanks again for the kind words 😃

[@danieltoo2008]

Wow!!! Now I can learn DS and Bioinformatics from a Thai Professional. Thanks Prof for helping get out off my SandBox prison mindset.😅😅😅

[@ElijahErureh]

I want to show my sincere appreciation for how you made data science so simple for me and interesting

[@DataProfessor]

Thanks for the kind words, this means a lot!

[@Yoursleepassistant]

What an awesome explanation I finally maneged to find channel to walk me through step by step. I sincerely thank you

[@DataProfessor]

Happy to hear that, you're welcome!

[@manabendraborah8654]

sir....thank you so much for simply sharing your knowledge.

[@saraalm9567]

This is incredible. Thank you so much for sharing your knowledge and experience with us!

[@gauravbhattacharjee5737]

Professor, this is an indispensable resource! You are the best!

[@DataProfessor]

Happy to help! Thanks for the kind words!

[@FarisIzzaturRahman]

I watch this on May 2021, and sooo excited with this amazing project video, what a great content, thankss Prof!

[@DataProfessor]

Glad you enjoyed it!

[@mr.harambae]

Yess! Finally! The niche teach professor!

[@avoniadevile3035]

I am new to your profile. I was intrested to see about drug discovery and especially l am rescently got interested in bioinformatics. Sadly l think l chose the wrong course as I am biomedical science student in my second years and now l can see that l should have gone bioinformatics way! It was very straight forward lesson, proffessor! Thank you so much

[@DataProfessor]

Hi, thanks for the comment. It's okay, I was also a biomed student back in the days. You'll get a solid domain knowledge of the biomedical sciences. You can also do bioinformatics in the side.

[@ingyghanm5402]

As an MSc student, I found this playlist very helpful. Can you share your experience writing scientific papers? I'm feeling lost!

[@alvinmodales6809]

You are so amazing data professor, thank for always sharing your expertise and knowledge

[@DataProfessor]

You are very welcome

[@raedhanoon2791]

This was a useful, informational video! It was straightforward and very interesting to learn about. You've intrigued me to pursue a bioinformatics program and I plan on starting my own project using the same tools demonstrated, Thanks Data Professor!

[@DataProfessor]

Glad it was helpful!

[@onkarkumbhar1610]

This is one only resource condensed, thanks!

[@DataProfessor]

Thank you for watching and support!

[@JellaMaruti]

Hello Dr Chanin, What if the units for IC50 are different? I am trying to create a project but the imported data from the ChEMBL contains different units (uM and nM). How to solve this problem? I went through one of your comment, but could not find the code in the notebook that you mentioned. Thank you for the help!

[@DataProfessor]

Hi, you’ll need to convert the units to the same scale by either converting uM (micro-molar or 10^-6) to nM (nano-molar or 10^-9) or vice versa.

[@delilahjones6496]

I would really appreciate it if you explained your lines of code and how they work. Otherwise, I am not learning why I'm typing what I'm typing, or why it's necessary, etc. I just watched another series by a different guy who thoroughly explained every line of code he wrote in R and I walked away with a much better understanding of why each line of code is being typed or why certain arguments were used.

[@DataProfessor]

Thanks for the feedback 😊

[@flowstateofmind2380]

ตามมาจากช่อง Data rockie นะครับ อยากสนับสนุนให้อาจารย์เขียนหนังสือด้าน data science for bioinformatics มากเลยครับ จะรอซื้อครับ 👍

[@anjelidubey1095]

What a great video! This helps so much in getting started building my portfolio

[@priyankachauhan9513]

Hello sir i am not able to run the githubtools to calculating the network proximity of bladder and colorectal cancer so please 🙏 make a video on this

[@salikmalik7631]

Great video data professor, waiting for part 2.. :)

[@aashishkatyal]

Awesome Tutorial Must Watch for Beginners.

[@DataProfessor]

Glad you think so! Thank you for watching!

[@Hiraeth_hiraeth]

are there any prerequisites to be able to do this project? like are we supposed to know some ML beforehand?

[@anjuzoldyck9266]

thank you so much professor you are a gem 💎

[@kamalikabhattacharjee336]

This is so good for self learners like me, thanks for creating this kind of bioinformatics content. Apart from acetylcholinesterase what are other molecules for which I can create similar project ? Tried for human BRCA1 but not a great one to create the exact similar project. Please suggest a few options.

[@khushboodutta30]

Even I'm interested to learn to build a project for HER 2 /BRCA1 / Bcr-Abl genes

[@DataProfessor]

Members in the Cytochrome P450 and Kinase protein family are also worth exploring

[@varshak4824]

Excellent and Awesome.I will share this tutorials with my friends. Sir, I have a request. Could you please make tutorial on how to collect data from BioLip, KEGG, PDBSUM etc and how to use various packages and tools such as Rcpi, Protr, PyPDI,Biopython, etc to generate descriptors? Just waiting for the second part. Many thanks!!!

[@DataProfessor]

Thanks Varsha for the suggestions. Currently in the making is how to use BioPython to do a protein blast. More on the molecular descriptors is also in the pipeline in forthcoming videos of the Bioinformatics Project series. 😃

[@shwetaredkar734]

@@DataProfessorthat's a great news. 👍

[@marcofestu]

Eager to see part 2 professor 😁

[@kampco9982]

I am trying to do follow along, doing this with dopamine d2 receptor protein, but after pre-processing the data, i noticed that there are some duplicate values that have the same molecule_chembl_id, but different standard_value, is this normal?

[@benjamintwumasi2480]

At the importing Library section of the Colab, I still get a messages like "No module named 'chembl_webresource_client". Please look into that.

[@DataProfessor]

Have you installed this library before running the code cell.

[@benjamintwumasi2480]

@@DataProfessor Yeah, that day I realised the mistake is from my end.

[@belkhiranesrine185]

Please sir, how can I solve this error, I have Windows 8.1 and I use python 3: ERROR: Cannot uninstall 'PyYAML'. It is a distutils installed project and thus we cannot accurately determine which files belong to it which would lead to only a partial uninstall.

[@aliqaitoon9965]

Great lecture. Thanks professor. Please we need second part soon 🙏😍

[@DataProfessor]

Ali, glad you found the video helpful. I'm also thrilled to make the next part, please stay tuned 😃

[@aliqaitoon9965]

@@DataProfessor i will be

[@PrarthanaKandwal]

Hello! I am working on a drug target interaction prediction using ML project. I wanted to know if I can use the data for my project in the same way given by you?

[@TejasriSivapriya]

Hi sir I am actually a biotechnology student and want to step into bioinformatics and have no prior knowledge about coding so do you thing this playlist is a good start and what else do you think I should do after this to understand more

[@johntichenor1601]

Hey there I'm getting an attribute error when setting target = new_client.target do you know the reason for this?

[@UwU-uq9pq]

Hi Professor, I have face a problem when following your code on Google Colab. While at the first step of copying files to Google Drive, I encounter a “ModuleNotFoundError”. And I found that this is cause by a module 'termios' which is only available on Unix system. I found that you are also using Windows OS but how can you solve the problem faced? Regarding this problem, the googled result only show me to change to unix os.

[@ramkumarrs1170]

Wow! super step by step process explanation!

[@DataProfessor]

Glad it was helpful! 😃

[@コルコル-n2u]

hello! can you help me? im having this kind of error when importing the libraries: ImportError: cannot import name 'hashlib' from 'requests_cache.backends.base' (/usr/local/lib/python3.7/dist-packages/requests_cache/backends/base.py) do you know why this happening?

[@コルコル-n2u]

this error comes when i execute: from chembl_webresource_client.new_client import new_client thanks for the guidance

[@DataProfessor]

Hi @VxS replied to your other post

[@rhard007]

Hi Professor can you recommend some books for self-study on the topic of bioinformatics? thank you.

[@DataProfessor]

Hi, there are quite a few books,the O'Reilly book "Bioinformatics Programming Using Python: Practical Programming for Biological Data" seems like a good starter to get you started with python coding bioinformatics examples.

[@devarakondahimaja8423]

If i want to write a if statement where the id number in row(1) of a CSV file is == id number in my text file print the sequence that means print the information of that particular id How to write?

[@garrettmccue2644]

creating the df from the bioactivity data dictionary is taking a long time (30+min) with no luck. Any suggestions on speeding this up? i am using jupyter fyi

[@sakichan2640]

thank you professor ! Do more bioinformatics video pls

[@DataProfessor]

Sure thing! More to come

[@Its_InduB]

Hi. Can you suggest tutorial for gRNA and target sequence designing besides online tools available. And working on resulting data after that.

[@ashwins5180]

Thanks alot sir...please upload part 2, i m eagerly waiting for ur next video for bioinfo projects in ml😍😍😍

[@DataProfessor]

Thanks Ashwin, it was fun making this video, I will also release a Part 0 video (introductory video on the biology background) as well 😃

[@nikitia_r]

Hi Prof Chanin, When I run this code in JupyterNotebook, I get stuck where we save the bioactivity data. I run the following: df.to_csv('C:/Users//bioactivity_data.csv') df = pd.read_csv("bioactivity_data.csv") # to read the csv df.head(5) # to view the data while the I am able to access the csv on my desktop , the code doesnt run in the notebook. (still shows In [*]: at df.to_csv... I would just like to find out if there are any suggestions as to how I should be doing this?

[@DataProfessor]

Hi, You could try removing the path so that you have df.to_csv('bioactivity_data.csv') and see if this works

[@arkadeepbanerjee2347]

Looking forward to part 2.

[@DataProfessor]

Arkadeep, thanks for the comment! Part 2 is in the making.

[@mohtashimnizamani]

It'll be studying computer science at university and I'm also interested in bioinformatics, but I don't have any biology background whatsoever. How should I approach bioinformatics and can I self study biology concepts and start doing bioinformatics projects?

[@eyupbilgi3191]

thank you for this amazing introduction. is it possible to use same approach to collect data from article repositories like elsevier, sciencedirect, scopus etc. with certain keywords and endpoints.

[@DataProfessor]

Similar concept applies but instead of the chembl API you can look into using the API of these article repositories.

[@koussaisalem4894]

why did u use IC50 to work on?why dont u use all the features?

[@DishaanChahal]

Hi, if any of my fellow bioinformaticians is watching this video. Let me know how does it help? I don't mean anything negative. The video seems great. But here you have already built a project and are running it in front of us. How do I build one of my own? Could you please teach us that? Or is this how people generally take inspiration about making projects? I am sorry I ma very new to this.

[@sebastiancastro4126]

Hello, I would like to make an inquiry. When we obtain the dataframe with the data for the biological activity of the selected target, some numeric columns are "object", which prevents statistics from being performed. How can I change the dtype of these columns? Thank you very much!

[@elshroomness]

I am having an issue trying to install the chembl resource client. This the error that i am running into: ""ERROR: Cannot uninstall 'PyYAML'. It is a distutils installed project and thus we cannot accurately determine which files belong to it which would lead to only a partial uninstall. "" Can anyone help? EDIT: I uninstalled Anaconda and reinstalled it and its working fine.

[@cooldayka]

Dear Professor, Is it possible to somehow contact you, I have a small question about one thing not really about the topic but about the course that is available I am now a bit confused should I pay for it or better to not do it, since it most probably will not be much beneficial

[@DataProfessor]

Hi you contact me at [e-mail]

[@TravisKPHall]

Dear Professor, this was an amazing tutorial and lecturer in one, thank you so much, but I have two questions, I am currently trying to create my own independent model and I have a question, the classification of active, inactive or intermediate based on the IC50 value that you used, is this a universally accepted for all molecules when making a QSAR model? What constitutes us using these parameters active 10000?

[@adityakoushik5726]

hello great tutorial! Is it possible to do this method with your own target protein (not from chembl)?

[@DataProfessor]

No for Part 1 of this series, this is for target protein that is available on the ChEMBL database. Yes to Part 2 and beyond where you can use whatever dataset that you may have compiled from other databases (PubChem or manually from the literature) and follow the same workflow.

[@ArvindPandeyeng]

Can you post the link of the research paper you were referring?

[@narendra_nn]

Hello, In recent version of Chembl(v29) database there is a target SARS-Cov2 with Chembl Id of CHEMBL4523582; In this dataset there is a feature of Standard type containing inhibition (~98% of data) and IC50(~2% of data) as classes, I am pleased to know the difference between them or can i see those both as a same standard type....

[@krishnaprasad3726]

Sir , where is the previous part of this video.. please provide me the link 🙏

[@gayathrim3022]

Could you please post a video on extracting various important information say chemical, ADR etc related to the drug using NLP techniques.

[@DataProfessor]

Thanks for the suggestion, will definitely consider this for future videos.

[@abolajishiwoku32]

As an aspiring data scientist, this project has been really helpful in building my portfolio with original data. Do you think building a portfolio of projects based on past academic papers is useful in today's biotech industry ?

[@DataProfessor]

Yes, definitely. The existing research community is based on doing cutting edge research that is based on past academic papers. The goal is to find knowledge gaps presented in the current research literature and to make incremental improvements that would lead to publishing the work itself as a research paper. Hope this helps.

[@naganandhireddygunreddy5397]

how to create a data folder in jupyter notebook and copy bioactivity_data csv file...please help me how do this part in jupyter notebook..help me out i got strucked at this part....in this video , how to create and copy explained colab notebooks on google drive

[@alizanaz5963]

Hi! I have been following your tutorials from past few days. I have a question. Is it necessary to test models on the same dataset they were trained with, or can a different test dataset be used for evaluation?

[@halizahasniaputri8869]

I'm doing my final project for my graduation later, I thought of various ways and I didn't find any way out until I finally found your video, I'm very grateful that you made a video like this, it really helped me. May I ask a few things? how do you combine two chemical molecules so that you get a new molecular structure and then test the bioinformatics? I am very confused about that, please help me Can I talk about this with you please? Thank you very much..

[@ias....burningdreamofmylif5516]

Have you done your project by this playlist?

[@sebastianjorgecastro2452]

Hello, when I use df = pd.DataFrame.from_dict(res), I get this error: TypeError: Object of type DataFrame is not JSON serializable. What can I do? Thank you!

[@DataProfessor]

Can you recheck if you have run all cells in sequential order

[@sebastianjorgecastro2452]

@@DataProfessor My mistake! I didn't select the target correctly.

[@angsumandas1]

Sir I tried hard to use these techniques to Autoimmunity and allergenic drug target. But I did not succeed. Please show me oath!

[@Activistxpeace]

Dear data professor and channel fans. I am a biologist and new to bioinformatics. I am trying to use your videos and code to run experiments to learn. When I open Google colab and open the data professor notebook in code/python I can't see anything. Can you please explain to me if I need to install python in my computer to use Google colab? What other basic programs I need to be able to see the notebook and code? Is the code still available? If anyone can help me solve this questions to I can replicate this experiment I appreciate it very much. Thank you.

[@hermainrais2280]

Hello everyone can anyone please tell where i can find only computational based working article found in Bioinformatics?

[@casualmaythamforaveragestu2616]

What kind of pc I can work on can you give me a spec??

[@naturevideosandaudiostv3262]

Sir every video of u is a new lesson for us but plz if u dont min plz zoom the vid. So that we can see the code clearly plz

[@DataProfessor]

Thanks for suggestion, recent videos are zoomed in, sorry for the small font size of earlier videos.

[@samarafroz9852]

You're doing such a great job sir please upload more tutorial about AI and drug discovery please upload drug design with GAN and AAE

[@DataProfessor]

Thanks for the suggestion!

[@samarafroz9852]

@@DataProfessor welcome sir

[@balamurganp7224]

As a college student, can i earn anything using bioinformarics by anymeans? 🤔

[@josefranklinct]

that's fantastic, thanks so much professor

[@DataProfessor]

Thanks for watching! Glad you liked it!

[@sadiafarzanadiya2800]

As a high school student it has gone beyond my head now I need some sleep

[@nguyenthanhtrung3768]

Specially thank you for your useful and practical video. It would be much more applicable if you could instruct how to execute this work with R.

[@DataProfessor]

Great suggestion! I'll definitely consider this for future videos. In the meantime, please refer to the GitHub and link to the research paper of one recent publication from our research group: github.com/chaninlab/anti-sickling pubs.rsc.org/en/content/articlelanding/2018/ra/c7ra12079f

[@nguyenthanhtrung3768]

@@DataProfessor Thank you very much for your valuable suggestions. It would be very helpful if you could advise how to download necessary data from several other databases to apply for other drug discover.

[@poojavani223]

This video really awesome, thank you so much.

[@saipavanchary0521]

Sir Subscribed just now!!

[@DataProfessor]

Thanks, welcome aboard 😄

[@andyderek3021]

Interesting tutorial! Please, I have a question: can someone explain to me why opt for "SINGLE PROTEIN" why not "Organism" ?

[@shraddhaverma4111]

Sir can you please recommend any for Computational chemistry !!!

[@sherin47]

Hi, I have completed Masters in Bioinformatics 12 yrs. before, With no prior practical experience. What would you suggest further for enhancing career and obtaining a job.

[@DataProfessor]

Hi, without prior experience may be a disadvantage if going to industry, I would suggest to find a local university and offer to do an internship or work for free to get break the gap period so that you have acquired some experience, perhaps help to complete a project. Afterwards you can start to look at other opportunities.

[@sherin47]

@@DataProfessor i needed some guidance in this area.Can you provide me your email id.Appreciate your support.

[@yinyang6058]

Thank you! This is soooooo helpful to me!!!

[@mnvny]

Sir Can you please briefly explain why we are choosing IC50?

[@DataProfessor]

Hi, IC50 is the bioactivity value that we use as the Y variable in model building.

[@LnPlayEng]

Secondly, what does assay type A, B means. Thanks

[@pradumnchavan1745]

thanks you sir for this amazing tutorial i am msc bioinformatics student can you plz make complete video on another bioinfo project using the approach text mining and data curation.

[@DataProfessor]

Thanks for suggestion 😃

[@idanmorad4769]

Try and use more Of pandas’ built in method such as map or apply instead of looping over the data frame

[@DataProfessor]

Thanks Idan for the valuable suggestion!

[@misganamengistu5503]

i was looking for to download files from pubchem just like you did in chembl , can you show me the web client code for pubchem database

[@DataProfessor]

Thanks for suggestion. I have also wanted to do that, but didn't get the chance to, let me prioritize this task for a future video.

[@misganamengistu5503]

@@DataProfessor thank you sir

[@luiseduardogoncalves2228]

Thank you professor for this tutorial! I am very new to bioinformatics and I would like to assure one thing. For example, when I type on ChEMBL a protein like Phospholipase A2 and then select targets, all of the results displayed are Phospholipase A2 targets right? Secondly, if i choose single protein, this means that the displayed protein is targeted by phospholipase A2. Is this correct?

[@e0n662]

Sir, can we also do the same with the zinc15 database?

[@DataProfessor]

ZINC can be used as a test set that can be used against a trained model for finding putative hits.

[@e0n662]

@@DataProfessor how many should be in my training set sir? Are 1000 compounds enough to make it reliable? Do you do live sessions also sir?

[@muditarora9860]

can we say IC50 is the ammount of drug required by a person, for treating his disease?????

[@DataProfessor]

In a way, yes! Its the concentration of the drug required to inhibit the target protein (inactivating it) at 50% capacity

[@eduardourbano4596]

very interesting. Great job!

[@DataProfessor]

Thanks for watching 😃

[@arvinths9025]

Sir, is these only for target types in chembl database or also for chembl compound types,tissue types, assay types, which is shown in search bar of chembl database?

[@DataProfessor]

Hi. We are searching for a "Target" of interest (a specific protein such as Aromatase) and the associated compounds that have been reported to bind to the target protein will be downloaded as our dataset.

[@nidhibharani1886]

Great video with concise explanation 👍 Is there a similar way to download sequencing data? Please make a video on that topic.

[@attabukhari7590]

Sir how to find protein sequences in bioinformtics tools

[@lotfibourougaa6209]

Hi Sir Can you share a research paper that talks about these approaches.

[@fahaddewtoniumfd5428]

Hi. Is there any prerequisite for fully understanding this video. I have an undergraduate biology background, with very little experience in programming. Will that be enough?

[@DataProfessor]

Yes absolutely, I go at the basic level that you can follow step by step in a guided way. I would recommend to also take an introductory python course via Kaggle mini-course to augment your understanding, please see this video also kzbin.info/www/bejne/kKW3pWtoZ8d3hKc

[@musicalrea5433]

Great video! I have a question: When we have Ki as standard_type, instead of IC50, what are the Ki intervals for labeling the compounds as active, inactive and intermediate?

[@DataProfessor]

Hi, Ki happens to have the same bioactivity range, so you can use the same threshold values.

[@musicalrea5433]

@@DataProfessor Great! Thank you so much Data Professor!!

[@positive51]

Thanks for what you do!

[@DataProfessor]

A pleasure, thanks for watching!