ChEMBL errata: Difference between revisions
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This is a page to keep track of errata we've found with the ChEMBL database at [https://www.ebi.ac.uk/chembldb/] | This is a page to keep track of errata we've found with the ChEMBL database at [https://www.ebi.ac.uk/chembldb/] | ||
These problems refer to ChEMBL11. Problems 4-9 have been attended to in the next release of ChEMBL, expected at the end of November. | |||
* 4. https://www.ebi.ac.uk/chembldb/index.php/compound/inspect/CHEMBL389012 | * 4. https://www.ebi.ac.uk/chembldb/index.php/compound/inspect/CHEMBL389012 | ||
Annotated as an Antagonist in ChEMBL, but abstract claims it is an agonist | Annotated as an Antagonist in ChEMBL, but abstract claims it is an agonist | ||
ChEMBL Help - This will not be changed and I will be sending you an email in due course to let you know why, but as it stands, the data is correct. | |||
* 5. CHEMBL293146 is 0 nM for O42392 according to assay CHEMBL818834 | * 5. CHEMBL293146 is 0 nM for O42392 according to assay CHEMBL818834 | ||
| Line 8: | Line 14: | ||
There are hundreds of these. examples. I will email them to you | There are hundreds of these. examples. I will email them to you | ||
ChEMBL Help - the value of 1x10^-12 that you have seen in the abstract is linked to the IC50 for this compound and the 0nM is linked to its Ki. As we do not have electronic access to the full paper, we cannot check this until we can track down a paper copy. The value of 1E-12 was changed a few weeks ago and will be visible in the next release. | |||
* 6. Compound CHEMBL1288160 is annotated at -4000 nM for O96013 | * 6. Compound CHEMBL1288160 is annotated at -4000 nM for O96013 | ||
ChEMBL Help - this should be % and will be changed | |||
and Compound CHEMBL1095696 is annotated at -14 nM for P25099 | and Compound CHEMBL1095696 is annotated at -14 nM for P25099 | ||
ChEMBL Help - this is taken directly from the paper, which states this as the Ki, with the units nM. | |||
There are hundreds of a couple of dozen of "negative IC50" values, below: | There are hundreds of a couple of dozen of "negative IC50" values, below: | ||
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accession molecule std units std value doc_id src_id | accession molecule std units std value doc_id src_id | ||
P14416 CHEMBL163087 nM -0.46 = 15817 1 | P14416 CHEMBL163087 nM -0.46 = 15817 1 | ||
P13612 CHEMBL330006 nM -0.5 = 5334 1 | P13612 CHEMBL330006 nM -0.5 = 5334 1 | ||
P13612 CHEMBL330006 nM -0.5 = 5334 1 | P13612 CHEMBL330006 nM -0.5 = 5334 1 | ||
P05556 CHEMBL330006 nM -0.5 = 5334 1 | P05556 CHEMBL330006 nM -0.5 = 5334 1 | ||
P05556 CHEMBL330006 nM -0.5 = 5334 1 | P05556 CHEMBL330006 nM -0.5 = 5334 1 | ||
P14416 CHEMBL162762 nM -0.51 = 15817 1 | P14416 CHEMBL162762 nM -0.51 = 15817 1 | ||
P20288 CHEMBL162762 nM -0.55 = 15817 1 | P20288 CHEMBL162762 nM -0.55 = 15817 1 | ||
P14416 CHEMBL162762 nM -0.55 = 15817 1 | P14416 CHEMBL162762 nM -0.55 = 15817 1 | ||
P14416 CHEMBL163087 nM -0.63 = 15817 1 | P14416 CHEMBL163087 nM -0.63 = 15817 1 | ||
P20288 CHEMBL163087 nM -0.65 = 15817 1 | P20288 CHEMBL163087 nM -0.65 = 15817 1 | ||
P13612 CHEMBL432215 nM -0.65 = 5334 1 | P13612 CHEMBL432215 nM -0.65 = 5334 1 | ||
P13612 CHEMBL432215 nM -0.65 = 5334 1 | P13612 CHEMBL432215 nM -0.65 = 5334 1 | ||
P05556 CHEMBL432215 nM -0.65 = 5334 1 | P05556 CHEMBL432215 nM -0.65 = 5334 1 | ||
P05556 CHEMBL432215 nM -0.65 = 5334 1 | P05556 CHEMBL432215 nM -0.65 = 5334 1 | ||
P35462 CHEMBL162762 nM -0.69 = 15817 1 | P35462 CHEMBL162762 nM -0.69 = 15817 1 | ||
P21917 CHEMBL162762 nM -0.69 = 15817 1 | P21917 CHEMBL162762 nM -0.69 = 15817 1 | ||
P35462 CHEMBL163087 nM -0.74 = 15817 1 | P35462 CHEMBL163087 nM -0.74 = 15817 1 | ||
P21917 CHEMBL163087 nM -0.76 = 15817 1 | P21917 CHEMBL163087 nM -0.76 = 15817 1 | ||
P25099 CHEMBL1088398 nM -1 = 51024 1 | P25099 CHEMBL1088398 nM -1 = 51024 1 | ||
P12931 CHEMBL451544 nM -1.9e+05 = 16451 1 | P12931 CHEMBL451544 nM -1.9e+05 = 16451 1 | ||
P12931 CHEMBL80333 nM -1.92e+05 = 16451 1 | P12931 CHEMBL80333 nM -1.92e+05 = 16451 1 | ||
P25099 CHEMBL1087078 nM -3 = 51024 1 | P25099 CHEMBL1087078 nM -3 = 51024 1 | ||
P35610 CHEMBL351272 nM -7.3e+04 < 2018 1 | P35610 CHEMBL351272 nM -7.3e+04 < 2018 1 | ||
P30543 CHEMBL1095696 nM -8 = 51024 1 | P30543 CHEMBL1095696 nM -8 = 51024 1 | ||
P30543 CHEMBL1087078 nM -10 = 51024 1 | P30543 CHEMBL1087078 nM -10 = 51024 1 | ||
P25099 CHEMBL1087079 nM -10 = 51024 1 | P25099 CHEMBL1087079 nM -10 = 51024 1 | ||
There are dozens more, maybe hundreds. | |||
ChEMBL Help: There only look to be dozens as there are duplicates in this list - there were only 12 in ChEMBL_10 and ChEMBL_11. There are now no negative IC50 values in the database. | |||
* 7. There are four target IDs in ChEMBL that have a NULL description. That would seem to be wrong, but there could be some purpose to doing this. e.g. "we have to come back to this later..." | |||
The TIDs are : 22226, 22222, 22224, 22228 | |||
ChEMBL Help: The TIDs of 22222 and 22224 are for ADMET and Nucleic Acid data. These do not have specific targets, and so, cannot be given a specific Target ID (TID). 22226 and 22228 are 'Unchecked' and 'Unknown', respectively, and 'Unchecked' means that they are in a holding place, waiting to be curated further. 'Unknown' means that they have been curated but a suitable TID cannot be found due to the limited data or information that we have. I have asked the biological curator to update the descriptions on these pages to make it more obvious for users. | |||
* 8. Functional activities with negative IC50s: (6 found) | |||
TID CHEMBL MOL ID Units number DOC ID SRC_ID | |||
80166 nM -1000 = 15748 1 | |||
81280 CHEMBL14691 nM -4400 = 12777 1 | |||
50594 CHEMBL25847 nM -9000 = 11189 1 | |||
22226 CHEMBL1649862 nM -22900 = 55281 1 | |||
50594 CHEMBL188 nM -35000 = 11189 1 | |||
50594 CHEMBL165733 nM -40000 = 8276 1 | |||
ChEMBL Help - the negative IC50s have now been changed, apart from 2 of them. These need to be double checked before they can be removed. | |||
* 9. There are easily 200 entries with zero IC50s. Here is a smattering. Full listing on request | |||
TID CHEMBL MOL ID Units number DOC ID SRC_ID | |||
80532 CHEMBL314934 nM 0 = 16464 1 | |||
80444 CHEMBL68765 nM 0 = 14961 1 | |||
80444 CHEMBL66975 nM 0 = 14961 1 | |||
80390 CHEMBL314934 nM 0 = 16464 1 | |||
80295 CHEMBL82829 nM 0 = 947 1 | |||
80285 CHEMBL117611 nM 0 = 12066 1 | |||
ChEMBL Help - whilst there are some data points that need to be changed in this list (and the one you sent me), the majority are curated 'as in the paper'. Whilst we understand that IC50s can't be 0, it is not our place to omit this information from curation if it is stated as such in the original publication. | |||
[[Category:Errata]] | [[Category:Errata]] | ||
[[Category:ChEMBL]] | |||
[[Category:Obsolete]] | |||
Latest revision as of 14:46, 21 March 2014
This is a page to keep track of errata we've found with the ChEMBL database at [1]
These problems refer to ChEMBL11. Problems 4-9 have been attended to in the next release of ChEMBL, expected at the end of November.
Annotated as an Antagonist in ChEMBL, but abstract claims it is an agonist
ChEMBL Help - This will not be changed and I will be sending you an email in due course to let you know why, but as it stands, the data is correct.
- 5. CHEMBL293146 is 0 nM for O42392 according to assay CHEMBL818834
In fact, it is 10^-12 M in the paper (or seems to me to be so. 10^-12 is small, but it is not the same as zero.
There are hundreds of these. examples. I will email them to you
ChEMBL Help - the value of 1x10^-12 that you have seen in the abstract is linked to the IC50 for this compound and the 0nM is linked to its Ki. As we do not have electronic access to the full paper, we cannot check this until we can track down a paper copy. The value of 1E-12 was changed a few weeks ago and will be visible in the next release.
- 6. Compound CHEMBL1288160 is annotated at -4000 nM for O96013
ChEMBL Help - this should be % and will be changed
and Compound CHEMBL1095696 is annotated at -14 nM for P25099
ChEMBL Help - this is taken directly from the paper, which states this as the Ki, with the units nM.
There are hundreds of a couple of dozen of "negative IC50" values, below:
accession molecule std units std value doc_id src_id
P14416 CHEMBL163087 nM -0.46 = 15817 1 P13612 CHEMBL330006 nM -0.5 = 5334 1 P13612 CHEMBL330006 nM -0.5 = 5334 1 P05556 CHEMBL330006 nM -0.5 = 5334 1 P05556 CHEMBL330006 nM -0.5 = 5334 1 P14416 CHEMBL162762 nM -0.51 = 15817 1 P20288 CHEMBL162762 nM -0.55 = 15817 1 P14416 CHEMBL162762 nM -0.55 = 15817 1 P14416 CHEMBL163087 nM -0.63 = 15817 1 P20288 CHEMBL163087 nM -0.65 = 15817 1 P13612 CHEMBL432215 nM -0.65 = 5334 1 P13612 CHEMBL432215 nM -0.65 = 5334 1 P05556 CHEMBL432215 nM -0.65 = 5334 1 P05556 CHEMBL432215 nM -0.65 = 5334 1 P35462 CHEMBL162762 nM -0.69 = 15817 1 P21917 CHEMBL162762 nM -0.69 = 15817 1 P35462 CHEMBL163087 nM -0.74 = 15817 1 P21917 CHEMBL163087 nM -0.76 = 15817 1 P25099 CHEMBL1088398 nM -1 = 51024 1 P12931 CHEMBL451544 nM -1.9e+05 = 16451 1 P12931 CHEMBL80333 nM -1.92e+05 = 16451 1 P25099 CHEMBL1087078 nM -3 = 51024 1 P35610 CHEMBL351272 nM -7.3e+04 < 2018 1 P30543 CHEMBL1095696 nM -8 = 51024 1 P30543 CHEMBL1087078 nM -10 = 51024 1 P25099 CHEMBL1087079 nM -10 = 51024 1
There are dozens more, maybe hundreds.
ChEMBL Help: There only look to be dozens as there are duplicates in this list - there were only 12 in ChEMBL_10 and ChEMBL_11. There are now no negative IC50 values in the database.
- 7. There are four target IDs in ChEMBL that have a NULL description. That would seem to be wrong, but there could be some purpose to doing this. e.g. "we have to come back to this later..."
The TIDs are : 22226, 22222, 22224, 22228
ChEMBL Help: The TIDs of 22222 and 22224 are for ADMET and Nucleic Acid data. These do not have specific targets, and so, cannot be given a specific Target ID (TID). 22226 and 22228 are 'Unchecked' and 'Unknown', respectively, and 'Unchecked' means that they are in a holding place, waiting to be curated further. 'Unknown' means that they have been curated but a suitable TID cannot be found due to the limited data or information that we have. I have asked the biological curator to update the descriptions on these pages to make it more obvious for users.
- 8. Functional activities with negative IC50s: (6 found)
TID CHEMBL MOL ID Units number DOC ID SRC_ID
80166 nM -1000 = 15748 1 81280 CHEMBL14691 nM -4400 = 12777 1 50594 CHEMBL25847 nM -9000 = 11189 1 22226 CHEMBL1649862 nM -22900 = 55281 1 50594 CHEMBL188 nM -35000 = 11189 1 50594 CHEMBL165733 nM -40000 = 8276 1
ChEMBL Help - the negative IC50s have now been changed, apart from 2 of them. These need to be double checked before they can be removed.
- 9. There are easily 200 entries with zero IC50s. Here is a smattering. Full listing on request
TID CHEMBL MOL ID Units number DOC ID SRC_ID
80532 CHEMBL314934 nM 0 = 16464 1 80444 CHEMBL68765 nM 0 = 14961 1 80444 CHEMBL66975 nM 0 = 14961 1 80390 CHEMBL314934 nM 0 = 16464 1 80295 CHEMBL82829 nM 0 = 947 1 80285 CHEMBL117611 nM 0 = 12066 1
ChEMBL Help - whilst there are some data points that need to be changed in this list (and the one you sent me), the majority are curated 'as in the paper'. Whilst we understand that IC50s can't be 0, it is not our place to omit this information from curation if it is stated as such in the original publication.