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Disable CORD transform until URL issue is sorted #87

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merged 3 commits into from
Apr 10, 2020
Merged

Disable CORD transform until URL issue is sorted #87

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eadc04c
Disable CORD transform until URL issue is sorted
justaddcoffee Apr 10, 2020
43bd636
Removed WIP transform
justaddcoffee Apr 10, 2020
4ddc6fe
Merge from master
justaddcoffee Apr 10, 2020
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16 changes: 8 additions & 8 deletions download.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -73,14 +73,14 @@
#
# SciBite CORD-19 annotations v1.2
#
-
url: https://s3.eu-west-2.amazonaws.com/scibite.covid19data/CORD19/annotated-cord19/CORD-19_1_3.zip
local_name: CORD-19_1_3.zip

# SciBite CORD-19 entity co-occurrences v1.0
-
url: https://github.com/SciBiteLabs/CORD19/raw/master/sentence-co-occurrence-CORD-19/1.0/cv19_scc.zip
local_name: cv19_scc.zip
#-
# url: https://s3.eu-west-2.amazonaws.com/scibite.covid19data/CORD19/annotated-cord19/CORD-19_1_3.zip
# local_name: CORD-19_1_3.zip
#
## SciBite CORD-19 entity co-occurrences v1.0
#-
# url: https://github.com/SciBiteLabs/CORD19/raw/master/sentence-co-occurrence-CORD-19/1.0/cv19_scc.zip
# local_name: cv19_scc.zip

#
# PharmGKB - drug -> drug target info, and gene id mappings
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4 changes: 2 additions & 2 deletions kg_covid_19/transform.py
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Expand Up @@ -7,7 +7,7 @@
from kg_covid_19.transform_utils.hpo.hpo import HpoTransform
from kg_covid_19.transform_utils.\
sars_cov_2_gene_annot.sars_cov_2_gene_annot import SARSCoV2GeneAnnot
from kg_covid_19.transform_utils.scibite_cord import ScibiteCordTransform
# from kg_covid_19.transform_utils.scibite_cord import ScibiteCordTransform
from kg_covid_19.transform_utils.pharmgkb import PharmGKB
from kg_covid_19.transform_utils.string_ppi import StringTransform
from kg_covid_19.transform_utils.ttd.ttd import TTDTransform
Expand All @@ -20,7 +20,7 @@
'HpoTransform': HpoTransform,
'TTDTransform': TTDTransform,
'StringTransform': StringTransform,
'ScibiteCordTransform': ScibiteCordTransform,
# 'ScibiteCordTransform': ScibiteCordTransform,
'PharmGKB': PharmGKB,
'SARSCoV2GeneAnnot': SARSCoV2GeneAnnot
}
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