24.06 docs and comms

[buniello]

This ticket will summarise all tasks related to documentation and communication for the 24.06 Platform/PPP release. Some initial notes:

Platform

• [x] AOTF UI changes
  • Uploads
  • uploads and pinning behaviour
  • Reset button
• [x] New burden tests (3 new publications)
• [x] Including AZ PheWAS Portal 470k
• [x] New ChEMBL 34, Clinical trails data, tractability data
• [x] GEL PanelApp updates and community issue
• [x] Data updates

PPP

• [ ] Target Networks Interactions
• [x] Facet search - User testing tickets
• [x] New data
  • VL
  • Predicted pockets
  • iFuncOnc
  • DNA damage

Others

• [x] Metrics

[buniello]

@ireneisdoomed would you be able to draft doc changes for new burden test please?

[HelenaCornu]

I have drafted the release post, please could you take a look?

@ireneisdoomed, please could you help me find an example of:

• a new EMA drug from ChEMBL 34? (ideally one only approved by EMA). TEMOPORFIN? TOCOPHERSOLAN? ALIPOGENE TIPARVOVEC?
• evidence from the G2P skeletal panel? Done — POP1 in anauxetic dysplasia, first evidence from Gene2Phenotype

[HelenaCornu]

@ireneisdoomed For gene burden evidence, can I also check:

I wrote "Thanks to this update, we integrate an additional 10,315 evidence, with gene burden evidence for this source for a total of 9,004 unique target/phenotype pairs" but the total increase in evidence from the streamlit metrics is 8991.

Please can you tell me the number of new evidence from the AZ Phewas portal update, and how many target/phenotype pairs this affects?

[ireneisdoomed]

a new EMA drug from ChEMBL 34? (ideally one only approved by EMA). TEMOPORFIN? TOCOPHERSOLAN? ALIPOGENE TIPARVOVEC?

Those were already covered by other souces.

There are only 49 new drugs whose provenance comes only from the EMA list of approved drugs (15 in the evidence set). It was interesting to find a relevant example to use, because most of them are salts of other drugs already in the Platform. I thought eladocagene exuparvovec (Upstaza) can be interesting to illustrate because:

• it is a gene therapy
• it is indicated for Aromatic L-Amino Acid Decarboxylase deficiency, a rare disease that leads to developmental issues
• it was recently approved, in 2022

I hope this is a good one, here you have the full list

``` +-------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ |id |name | +-------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ |CHEMBL1200498|ALATROFLOXACIN MESYLATE | |CHEMBL1200553|CUPRIC CHLORIDE | |CHEMBL1201197|ALATROFLOXACIN | |CHEMBL1201692|FOLLITROPIN ALFA | |CHEMBL2096648|UREA C 13 | |CHEMBL2096660|SAMARIUM SM 153 LEXIDRONAM PENTASODIUM | |CHEMBL2103739|EMEDASTINE DIFUMARATE | |CHEMBL2108021|BESILESOMAB | |CHEMBL2108157|VOTUMUMAB | |CHEMBL2108253|ARCITUMOMAB | |CHEMBL2108290|EPOETIN THETA | |CHEMBL2108809|SULESOMAB | |CHEMBL2109036|IGOVOMAB | |CHEMBL2109093|EPOETIN DELTA | |CHEMBL2110561|SAMARIUM LEXIDRONAM PENTASODIUM | |CHEMBL4298167|FILGOTINIB MALEATE | |CHEMBL4298189|ELADOCAGENE EXUPARVOVEC | |CHEMBL5315049|SITAGLIPTIN FUMARATE | |CHEMBL5315050|ATOSIBAN ACETATE | |CHEMBL5315051|YTTRIUM CHLORIDE Y-90 | |CHEMBL5315052|RASAGILINE TARTRATE | |CHEMBL5315053|PEMETREXED MONOHYDRATE | |CHEMBL5315054|ERTUGLIFLOZIN PIDOLATE | |CHEMBL5315055|NALMEFENE HYDROCHLORIDE DIHYDRATE | |CHEMBL5315056|NALOXONE HYDROCHLORIDE DIHYDRATE | |CHEMBL5315061|CUPRIC CHLORIDE ANHYDROUS CU-64 | |CHEMBL5315062|LUTETIUM CHLORIDE LU-177 | |CHEMBL5315064|FOLLITROPIN DELTA | |CHEMBL5315067|AUTOLOGOUS PERIPHERAL-BLOOD MONONUCLEAR CELLS INCLUDING A MINIMUM OF 50 MILLION AUTOLOGOUS CD54+ CELLS ACTIVATED WITH PROSTATIC ACID PHOSPHATASE GRANULOCYTE-MACROPHAGE COLONY-STIMULATING FACTOR | |CHEMBL5315068|DINUTUXIMAB BETA | |CHEMBL5315069|DAMOCTOCOG ALFA PEGOL | |CHEMBL5315071|TUROCTOCOG ALFA PEGOL | |CHEMBL5315076|ALBUTREPENONACOG ALFA | |CHEMBL5315077|TILMANOCEPT | |CHEMBL5315078|EPTACOG BETA (ACTIVATED) | |CHEMBL5315079|DEPREOTIDE TRIFLUOROACETATE | |CHEMBL5315080|BULEVIRTIDE ACETATE | |CHEMBL5315084|PANCREAS POWDER, PORCINE | |CHEMBL5315089|DEFATTED POWDER OF ARACHIS HYPOGAEA L., SEMEN (PEANUTS) | |CHEMBL5315092|AUTOLOGOUS CULTURED CHONDROCYTES | |CHEMBL5315093|AUTOLOGOUS CD34+ ENRICHED CELL FRACTION THAT CONTAINS CD34+ CELLS TRANSDUCED WITH RETROVIRAL VECTOR THAT ENCODES FOR THE HUMAN ADA CDNA SEQUENCE | |CHEMBL5315097|ALLOGENEIC T CELLS GENETICALLY MODIFIED WITH A RETROVIRAL VECTOR ENCODING FOR A TRUNCATED FORM OF THE HUMAN LOW AFFINITY NERVE GROWTH FACTOR RECEPTOR (DELTALNGFR) AND THE HERPES SIMPLEX I VIRUS THYMIDINE KINASE (HSV-TK MUT2)| |CHEMBL5315099|EX VIVO EXPANDED AUTOLOGOUS HUMAN CORNEAL EPITHELIAL CELLS CONTAINING STEM CELLS | |CHEMBL5315113|SPHEROIDS OF HUMAN AUTOLOGOUS MATRIX-ASSOCIATED CHONDROCYTES | |CHEMBL5315115|LASOFOXIFENE TARTRATE | |CHEMBL5315126|FOLLITROPIN BETA | |CHEMBL5316164|YTTRIUM CHLORIDE | |CHEMBL5316165|LUTETIUM CHLORIDE | |CHEMBL561157 |TREPROSTINIL SODIUM | +-------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ ```

[ireneisdoomed]

I wrote "Thanks to this update, we integrate an additional 10,315 evidence, with gene burden evidence for this source for a total of 9,004 unique target/phenotype pairs" but the total increase in evidence from the streamlit metrics is 8991.

The total number of AZ evidence is 21,300. This is 9,533 more than in the previous release.

In terms of associations, we have practically doubled up to 4,419 (184% increase).

This varies from the total increase you report because Genebass evidence has slightly decreased after a user request to drop some evidence (minus ~600).

[HelenaCornu]

Amazing, thank you!

[HelenaCornu]

@ireneisdoomed would you be able to draft doc changes for new burden test please?

I have done this: https://platform-docs.opentargets.org/evidence#gene-burden Any issues let me know