Another Japan in the World

Jun Aruga's blog.

EMBL-EBI resources: An introduction

I watched this video today.

Introduction to EMBL EBI resources www.youtube.com

Literally this video is great to understand the data sources in the view of bird eyes. The detail page is here [1].

EBI Search

Example: Search by the gene name: "BRCA1".

  1. Go to EBI's top page. [2]
  2. Search "BRCA1" (= gene name) on the text field "Find a gene, protein or chemical".

    f:id:happybirthday:20181001051842p:plain Image source: EMBL-EBI

  3. Move to "Search results for BRCA1" page.

    f:id:happybirthday:20181001051941p:plain Image source: EMBL-EBI

  4. Click "Gene & protein summaries" > "BRCA1, DNA repair associated" link.
  5. Move to "Gene & protein summary for BRCA1" page. (https://www.ebi.ac.uk/s4/summary/molecular?term=BRCA1&classification=9606&tid=nameOrgENSMUSG00000017146)

    Gene f:id:happybirthday:20181001052012p:plain Image source: EMBL-EBI

  6. Click Expression button.

    Expression f:id:happybirthday:20181001052033p:plain Image source: EMBL-EBI

  7. Click Protein Structure button.

    Protein Structure f:id:happybirthday:20181001052043p:plain Image source: EMBL-EBI

Europe PMC

Europe PMC = PubMed Central connected with EBI's databases. [3]

10th Anniversary Treasure Hunt

The Treasure Hunt URL is here. [4] It seems that it is the fun content to learn the EBI's data resources.

f:id:happybirthday:20181001052642p:plain Image source: EMBL-EBI - 10th Anniversary Treasure Hunt [4]

Below image is great to know the resources in bird-eyes view.

f:id:happybirthday:20181014222254p:plain Image source: EMBL-EBI - 10th Anniversary Treasure Hunt [5]

References

The Open Targets

Today I want to introduce the genome service "Open Targets" [1], that I knew 2 month ago in a bio hackathon event at Genome Campus, Cambridge UK.

Summary

It is to find a drug "targeting" a gene. The philosophy of the service is "open". So, the name is "Open Targets". The database for opened targeting drug information.

So, what is the new things for Open Targets? There are 2 points.

  1. In my understanding, most of the bio database is for the use in academic area. But this bio database is collaboration with medical industry. That means this service gives them direct benefit. The benefit is to specify drug from patient's gene data and disease. To provide personalized medicine. To give a better way to cure patient disease than before.

  2. The service's openness itself. A person in Open Targets is sharing their thoughts in below video.

Question: What does the "open" in Open Targets mean?

  • 2.1. The first is that all of the data, software, results of open targets are published and released in entire world use. And we think that's incredibly important, because there are key areas of early stages understanding disease mechanism, one of the best targets go after.
  • 2.2. And those are definitely best on collaboratively working together between academia industry. Because anyone company does not have the completely academia industries the wide range of expertise and the data that needed to make the decisions.

There is also a regulation about data, such as GDPR in EU. To unify the data in the world considering the situation, open data (public domain or open license) is useful way.

This bio service has additional 18 open bio databases [2]. That's the case of how to use the open database practically and effectively.

vimeo.com

How to use

It seems that Open Targets, the bio database has 3 main elements "Gene", "Disease" and "Drug".

The scenario is like this.

  1. A patient is diagnosed as a disease in the hospital.
  2. A patient does sequencing their genome data in a hospital. And know which gene in their genome data has variant, mutation or characteristic.
  3. Then Input: Disease/Gene, Output: Drug by the service Open Targets.
  4. A patient is prescribed more proper medicine by a doctor.

And I would share 3 search flow cases.

Search Flow 1: Disease -> Drug

Refer the tutorial video [3].

  1. Search "asthma" (= Disease name) on top page.
  2. Move to asthma's associations page "Table" tab. ( https://www.targetvalidation.org/disease/EFO_0000270/associations )
  3. Click "View disease profile" link.
  4. Move to the disease page. ( https://www.targetvalidation.org/disease/EFO_0000270 )
  5. Click "Drugs" title.
  6. Search "lamotrigine" on search area.
  7. Click "Drug" - "LAMOTRIGINE" link.
  8. Move to the drug summary page. ( https://www.targetvalidation.org/summary?drug=CHEMBL741 )

f:id:happybirthday:20181001004005p:plain Image source: Open Targets

Search Flow 2: Gene -> Drug

Refer the tutorial video [4].

  1. Search "IL13" (= Gene name) on top page.
  2. Move to IL13's associations page "Table" tab. ( https://www.targetvalidation.org/target/ENSG00000169194/associations )
  3. Click "View IL13 profile" link under the title.
  4. Move to (targeting) gene "IL13"'s page. ( https://www.targetvalidation.org/target/ENSG00000169194 )
  5. Click "Drugs" section.
  6. Search "TNX-650" on the search area.
  7. Click "TNX-650" link.
  8. Move to the drug "TNX-650"'s page. ( https://www.targetvalidation.org/summary?drug=CHEMBL2109466 )

Search Flow 3: Gene -> Disease -> Drug

Refer the tutorial video [5].

  1. Search "BRCA2" (= Gene name) on top page.
  2. Move to BRCA2's associations page "Table" tab. ( https://www.targetvalidation.org/target/ENSG00000139618/associations )
  3. Click right blue square next to the disease name "lung carcinoma". (column: "Overall association score")
  4. Move to the evidence page "Evidence for BRCA2 in lung carcinoma". ( https://www.targetvalidation.org/evidence/ENSG00000139618/EFO_0001071 ) Maybe "EFO_0001071" is ID of "lung carcinoma".
  5. Click "Somatic Mutations".
  6. Then the diseases are shown. In case of this URL, there is no drug in "Drugs" category.

References