EUbOPEN Web issueshttps://gitlab.ebi.ac.uk/chembl/eubopen/eubopen-web/-/issues2024-02-06T13:48:00Zhttps://gitlab.ebi.ac.uk/chembl/eubopen/eubopen-web/-/issues/79Document_IDs for SGC datasets2024-02-06T13:48:00ZEmma MannersDocument_IDs for SGC datasets
SGC asked to harmonise their documents (i.e. standardise and update the title, abstract). For FAIRness, the documents should remain stable. However, a large number of replicated SGC assays have been provided in different datasets across...
SGC asked to harmonise their documents (i.e. standardise and update the title, abstract). For FAIRness, the documents should remain stable. However, a large number of replicated SGC assays have been provided in different datasets across multiple releases, and will be merged for v33. When we merge the SGC assays, we'll be merging multiple assays linked to multiple documents into a single assay linked to a single document. Therefore, we could consider harmonising the documents at the same time since some documents will change anyway during the merges. For now, I will perform the merges and will not update the document that remains live, but it would be good to consider tidying this up at some point.
Example (Incucyte datasets):
The assays from three Incucyte datasets will be merged into a single set of assays.
There are three documents linked to these assays. After merges/assay downgrades, only a single document will be linked to the remaining live assay. The document that will remain live (as per the SGC suggested updates) is doc_ID 118026. However, this older document is missing authors, abstract etc. but these details were provided with the most recent document (doc_ID; 126208). It would make sense to map over the author, abstract information to the original document.
DOC_ID YEAR DOI CHEMBL_ID TITLE AUTHORS ABSTRACT RELEASE
118026 2021 10.6019/CHEMBL4689842 CHEMBL4689842 EUbOPEN Chemogenomics Library wave 1 30
122367 2022 10.6019/CHEMBL5058564 CHEMBL5058564 Tm Shift (DSF) assay results for EUbOPEN Chemogenomis Library 2 (Incucyte) 32
126208 2023 CHEMBL5303304 EUbOPEN Chemogenomics Library - IncuCyte EUbOPEN Cell Viability-IncuCyte assay results for EUbOPEN Chemogenomics Library: The InucyCyte Viability assay is used to investigate cytotoxicity over 24h. This first determinant as an in cell quality control of different compounds is based on confluence analysis by brightfield acquisition. Compounds are classfiied according to their calculated growth rate in healhty, cytostatic or cytotoxic.https://gitlab.ebi.ac.uk/chembl/eubopen/eubopen-web/-/issues/78Display of the EUBOpen ID in ChEMBL for SRC_ID 552024-02-06T13:41:44ZEmma MannersDisplay of the EUBOpen ID in ChEMBL for SRC_ID 55The EUBOpen ID is currently captured in the compound_key field within the COMPOUND_RECORDS table. It's also available within the CIDX, an internal compound identifer.
The EUBOpen ID includes a batch identifier and salt information in bo...The EUBOpen ID is currently captured in the compound_key field within the COMPOUND_RECORDS table. It's also available within the CIDX, an internal compound identifer.
The EUBOpen ID includes a batch identifier and salt information in both the compound_key and CIDX.
There have been discussions around whether we need the batch and salt information in the compound_key or whether this should be removed in ChEMBL. The CIDX will still contain this detail for use on the Gateway (to specify the compound batch used in a particular assay).https://gitlab.ebi.ac.uk/chembl/eubopen/eubopen-web/-/issues/77Legacy data - potential fixes2024-01-31T11:07:35ZEmma MannersLegacy data - potential fixeshttps://gitlab.ebi.ac.uk/chembl/eubopen/eubopen-web/-/issues/76Create a ranking system for Main Compounds.2024-01-23T12:18:07ZDavid MendezCreate a ranking system for Main Compounds.Things to amend after Midterm Reviewhttps://gitlab.ebi.ac.uk/chembl/eubopen/eubopen-web/-/issues/75Potential structure errors2024-01-12T10:29:02ZEmma MannersPotential structure errorsCases where a single EUBOpen_ID is associated with two distinct ChEMBL structures (not alternative forms e.g. salts) may need a review:
| EUBOpen ID | Differences in associated structures |
|------------|---------------...Cases where a single EUBOpen_ID is associated with two distinct ChEMBL structures (not alternative forms e.g. salts) may need a review:
| EUBOpen ID | Differences in associated structures |
|------------|-------------------------------------------------------|
| EUB0000710 | Connectivity differences |
| EUB0000195 | Stereochemical differences |
| EUB0000303 | Stereochemical differences |
| EUB0000752 | Connectivity differences |
| EUB0000308 | Connectivity differences |
| EUB0001072 | Connectivity differences |
| EUB0000544 | Stereochemical differences |
| EUB0000714 | Connectivity differences |
| EUB0000326 | Stereochemical differences |
| EUB0000289 | Connectivity differences |
| EUB0000753 | Stereochemistry, should not have crossed bond in ring |
| EUB0000301 | Connectivity differences |
| EUB0000033 | Stereochemical differences |
| EUB0000328 | Stereochemical differences |
| EUB0000741 | Stereochemical differences |
| EUB0001564 | Stereochemical differences |
| EUB0000119 | Stereochemical differences |
| EUB0000057 | Stereochemical differences |
| EUB0000739 | Stereochemical differences |
| EUB0000704 | Connectivity differences |
| EUB0000090 | Stereochemical differences |
| EUB0000332 | Connectivity differences |
| EUB0000291 | Connectivity differences |
| EUB0000312 | Connectivity differences |
| EUB0000316 | Connectivity differences |
| EUB0001565 | Stereochemical differences |
| EUB0000199 | Stereochemical differences |
| EUB0000264 | Stereochemical differences |
| EUB0000750 | Stereochemical differences |
A single ChEMBL_ID (structure) is associated with two distinct EUBOpen_IDs:
| EUBOpen_IDs associated with a single structure | Compound_name |
|------------------------------------------------|-----------------|
| EUB0000663 | Barasertib-HQPA |
| EUB0000125b | Barasertib-HQPA |
| | |
| EUB0000325a | I-BRD9 |
| EUB0000247b | I-BRD9 (GSK602) |
| | |
| EUB0001692aCl | BI 1002494 |
| EUB0001529aCl | BI01002494 |
| | |
| EUB0000308 | A_079 |
| EUB0002011a | A-967079 |
A single name is associated with two different structures:
| EUBOpen_ID | Same name associated with two structures/EUBOpen_IDs |
|-------------|------------------------------------------------------|
| EUB0000324a | LP99 |
| EUB0000227c | LP99 |
| | |
| EUB0000175a | 640 |
| EUB0000878a | 640 |
| | |
| EUB0001058a | Paclitaxel |
| EUB0001808a | Paclitaxel |
| | |
| EUB0000301c | BTZO-4 |
| EUB0001135a | BTZO-4 |
| | |
| EUB0000963a | Prostaglandin D2 |
| EUB0001834a | Prostaglandin D2 |
| | |
| EUB0000319a | BI-1230 |
| EUB0001182a | BI-1230 |Things to amend after Midterm Reviewhttps://gitlab.ebi.ac.uk/chembl/eubopen/eubopen-web/-/issues/73Create SETS2024-01-23T13:03:05ZDavid MendezCreate SETSA `SET` shall be a collection of `DOCUMENTS` that are not necessarily equal to the entirety of documents of a `SRC_ID` (but could be). In some cases a `SET` can also be created from a number of `DOCUMENTS` from more than one `SRC_ID`. `S...A `SET` shall be a collection of `DOCUMENTS` that are not necessarily equal to the entirety of documents of a `SRC_ID` (but could be). In some cases a `SET` can also be created from a number of `DOCUMENTS` from more than one `SRC_ID`. `SETS` are user-defined groups of docuemnts that have to be defined by the depositors or by the ChEMBL team (for other legacy data).
Implementing this new structure for the Gateway as well as ChEMBL will allow easier search queries as well as the achnowledgement of certain data to belong together.Things to amend after Midterm ReviewEloy FelixDavid MendezBarbara ZdrazilSandra HäberleEloy Felixhttps://gitlab.ebi.ac.uk/chembl/eubopen/eubopen-web/-/issues/72Improve table layout in small screens.2024-01-11T12:58:07ZDavid MendezImprove table layout in small screens.Things to amend after Midterm Reviewhttps://gitlab.ebi.ac.uk/chembl/eubopen/eubopen-web/-/issues/71Assay_category; check this is in sync between ChEMBL and Gateway2023-11-28T11:00:50ZEmma MannersAssay_category; check this is in sync between ChEMBL and GatewayTamas has recently annotated the assay category for both legacy SGC CGL data and for incoming data. We will be using the ‘assay_category’ field within ChEMBL to capture this annotation. We need to ensure that the assay_category in ChEMBL...Tamas has recently annotated the assay category for both legacy SGC CGL data and for incoming data. We will be using the ‘assay_category’ field within ChEMBL to capture this annotation. We need to ensure that the assay_category in ChEMBL is in sync with the Gateway.https://gitlab.ebi.ac.uk/chembl/eubopen/eubopen-web/-/issues/70Compounds - Strange behaviour in aggregation.2023-11-21T14:04:43ZDavid MendezCompounds - Strange behaviour in aggregation.Things to amend after Midterm Reviewhttps://gitlab.ebi.ac.uk/chembl/eubopen/eubopen-web/-/issues/69Assays - Strange behaviour in query.2023-11-21T14:05:32ZDavid MendezAssays - Strange behaviour in query.Things to amend after Midterm ReviewJuan Felipe Mosquera MoralesJuan Felipe Mosquera Moraleshttps://gitlab.ebi.ac.uk/chembl/eubopen/eubopen-web/-/issues/68Compounds - Interpretation of results2024-01-23T13:12:48ZDavid MendezCompounds - Interpretation of resultsThings to amend after Midterm Reviewhttps://gitlab.ebi.ac.uk/chembl/eubopen/eubopen-web/-/issues/67Compounds - Missing information for negative controls, which leads to “empty”...2023-11-21T14:05:44ZDavid MendezCompounds - Missing information for negative controls, which leads to “empty” links.Things to amend after Midterm Reviewhttps://gitlab.ebi.ac.uk/chembl/eubopen/eubopen-web/-/issues/65Organise the compound batches2024-02-20T12:56:41ZDavid MendezOrganise the compound batchesThings to amend after Midterm Reviewhttps://gitlab.ebi.ac.uk/chembl/eubopen/eubopen-web/-/issues/36Allow to search by related names and synonyms.2023-11-21T14:05:27ZDavid MendezAllow to search by related names and synonyms.Bay-826: If you search for the target DDR2, it´s not in the result list, also if you search for the long name Discoidin domain-containing receptor 2
Separate search function for each table?
If you search for a target which is part of th...Bay-826: If you search for the target DDR2, it´s not in the result list, also if you search for the long name Discoidin domain-containing receptor 2
Separate search function for each table?
If you search for a target which is part of the DSF panel or incucyte, all compounds are listed, not only the ones who have this as main targetThings to amend after Midterm ReviewDavid MendezJuan Felipe Mosquera MoralesDavid Mendez