add antibody developability from TDC #99
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add Antibody Developability from: https://tdcommons.ai/single_pred_tasks/develop/ for both: TAP SAbDab, Chen et al. Need some one to ensure two list that I convert to two columns. Thanks
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data/SAbDab_Chen/meta.yaml
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| - https://rb.gy/idkdqp | ||
| - https://rb.gy/b8cx8i |
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With URIs we mean links to ontologies, such as the ones you can find here https://bioportal.bioontology.org/ontologies/BAO?p=classes&conceptid=http://purl.obolibrary.org/obo/NCIT_C20604
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I removed those as they were not fitting our setup.
data/SAbDab_Chen/meta.yaml
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| description: "Antibody data from Chen et al, where they process from the SAbDab. \n From an initial dataset of 3816 antibodies, they retained 2426\ | ||
| \ antibodies\n that satisfy the following criteria: 1. \n have both sequence (FASTA) and Protein Data Bank (PDB) structure files,\n \ | ||
| \ 2. contain both a heavy chain and a light chain, and 3. \n have crystal structures with resolution < 3 Å. \n The DI label is derived\ | ||
| \ from BIOVIA's pipelines." |
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the linebreaks seems a bit awkward, do you have an idea where they come from?
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I guess that was the Ångström Å!
data/SAbDab_Chen/meta.yaml
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| - id: antibody_pdb_ID | ||
| type: Other |
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are those IDs chemically meaningful or just some identifier number?
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So should we keep them or remove them?
data/SAbDab_Chen/meta.yaml
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| - "@article{Chen2020,\n doi = {10.1101/2020.06.18.159798},\n url = {https://doi.org/10.1101/2020.06.18.159798},\n year =\ | ||
| \ {2020},\n month = jun,\n publisher = {Cold Spring Harbor Laboratory},\n author = {Xingyao Chen and Thomas Dougherty and\ | ||
| \ \n Chan Hong and Rachel Schibler and Yi Cong Zhao and \n Reza Sadeghi and Naim Matasci and Yi-Chieh Wu and Ian Kerman},\n \ | ||
| \ title = {Predicting Antibody Developability from Sequence \n using Machine Learning}}" | ||
| - "@article{Dunbar2013,\n doi = {10.1093/nar/gkt1043},\n url = {https://doi.org/10.1093/nar/gkt1043},\n year = {2013},\n\ | ||
| \ month = nov,\n publisher = {Oxford University Press ({OUP})},\n volume = {42},\n number = {D1},\n pages\ | ||
| \ = {D1140--D1146},\n author = {James Dunbar and Konrad Krawczyk and Jinwoo Leem \n and Terry Baker and Angelika Fuchs and Guy Georges\ | ||
| \ and Jiye Shi and\n Charlotte M. Deane},\n title = {{SAbDab}: the structural antibody database},\n journal = {Nucleic\ | ||
| \ Acids Research}}" |
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I'm also surprised by the linebreaks here
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I guess this also due to the Å? Anyway, fixed!
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for more information, see https://pre-commit.ci
for more information, see https://pre-commit.ci
for more information, see https://pre-commit.ci
for more information, see https://pre-commit.ci
for more information, see https://pre-commit.ci
for more information, see https://pre-commit.ci
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tap cleanup is incoming, will finish up later |
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I need to understand better if the identifier columns taken alone are enough - I do not think so |
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Discuss: Better use Å instead of nm! |
add Antibody Developability from:
https://tdcommons.ai/single_pred_tasks/develop/
for both:
TAP
SAbDab, Chen et al.
Need some one to ensure two list that I convert to two columns. Thanks