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commit 1f01b43
Merge: ec6b7d8 734cc6e
Author: Evan Morris <evandietzmorris@gmail.com>
Date:   Fri Jul 19 14:38:15 2024 -0400

    Merge pull request #232 from RobokopU24/binding-predicate-update

    Modified predicates affected by biolink:binds

commit 734cc6e
Author: Evan Morris <evandietzmorris@gmail.com>
Date:   Fri Jul 19 14:32:02 2024 -0400

    bumping parsing versions for binds refactor parsers

commit ec6b7d8
Merge: e44cae6 00c6627
Author: Evan Morris <evandietzmorris@gmail.com>
Date:   Fri Jul 19 14:28:50 2024 -0400

    Merge pull request #233 from RobokopU24/pharos_KL/AT

    Improving the KL/AT in Pharos

commit 00c6627
Author: Evan Morris <evandietzmorris@gmail.com>
Date:   Fri Jul 19 14:26:48 2024 -0400

    bumping parsing version

commit 766c5b7
Author: eKathleenCarter <163005214+eKathleenCarter@users.noreply.github.com>
Date:   Tue Jul 16 12:42:45 2024 -0400

    Update predicates.py

    forgot to revert changes for interacts_with. Will keep it unmodified until further clarification.

commit 4cb0188
Author: eKathleenCarter <163005214+eKathleenCarter@users.noreply.github.com>
Date:   Tue Jul 16 12:41:36 2024 -0400

    Update predicates.py after comments

    Made changes to reflect comments by Chris:

    1. Do not modify "ed50": f"RO:0002434" until we know where this predicate comes from.
    "But I guess the main point is that it makes no sense to have an ed50 between a chemical and a gene/protein. Is it possible to see whether we actually have any of these?"

    2. "gi50": f"RO:0002434" -> {DGIDB}:Inhibitor

    3. Do not modify "interacts_with"  until we know where this predicate comes from.
    I" guess it would be easier to be sure if we know the context in which "interacts-with" was found in our ingestss.

    (but I'd be tempted to put 2436 for this one)"

    Main take away: where do these predicates come from? Can we track down how this was generated?

commit 711ac5a
Author: Kathleen <ekcarter@renci.org>
Date:   Wed Jul 10 15:10:28 2024 -0400

    Improving the KL/AT in Phaors

commit a687f30
Author: Kathleen <ekcarter@renci.org>
Date:   Wed Jul 10 12:32:26 2024 -0400

    Modified predicates affected by biolink:binds

commit e44cae6
Merge: 7ba9538 fa8ebf0
Author: Evan Morris <evandietzmorris@gmail.com>
Date:   Wed Jun 26 16:38:02 2024 -0400

    Merge pull request #231 from RobokopU24/requirements.txt-patch

    Update requirements.txt

commit fa8ebf0
Author: beasleyjonm <85600465+beasleyjonm@users.noreply.github.com>
Date:   Wed Jun 26 16:37:03 2024 -0400

    Update requirements.txt

    Updated requests 2.32.0 -> 2.32.3
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EvanDietzMorris committed Jul 19, 2024
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38 changes: 19 additions & 19 deletions Common/predicates.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,43 +8,43 @@
"allosteric_antagonist": f"{DGIDB}:antagonist",
"allosteric_modulator": f"{DGIDB}:modulator",
"antagonist": f"{DGIDB}:antagonist",
"antibody": f"{DGIDB}:binder",
"antibody_binding": f"{DGIDB}:binder",
"antibody": f"RO:0002436",
"antibody_binding": f"RO:0002436",
"antisense_inhibitor": f"{DGIDB}:inhibitor",
"app_ki": f"RO:0002434",
"app_km": f"RO:0002434",
"binding_agent": f"{DGIDB}:binder",
"app_ki": f"RO:0002434", # apparent Ki? if so change to RO:0002436
"app_km": f"RO:0002434", # apperent Km? if so change to RO:0002436
"binding_agent": f"RO:0002436",
"blocker": f"{DGIDB}:blocker",
"channel_blocker": f"{DGIDB}:channel_blocker",
"ec50": f"{DGIDB}:agonist",
"ed50": f"RO:0002434",
"ed50": f"RO:0002434", # Effective Dose. Where does this predicate come from? CB (2024_07): "it makes no sense to have an ed50 between a chemical and a gene/protein"
"gating_inhibitor": f"{DGIDB}:gating_inhibitor",
"gi50": f"RO:0002434",
"gi50": f"{DGIDB}:Inhibitor", # Growth Inhibitor
"ic50": f"{DGIDB}:inhibitor",
"inhibitor": f"{DGIDB}:inhibitor",
"interacts_with": f"RO:0002434",
"interacts_with": f"RO:0002434", # Where does this predicate come from? Possiblely needs to be modified to RO:0002436
"inverse_agonist": f"{DGIDB}:inverse_agonist",
"ka": f"RO:0002434",
"kact": f"RO:0002434",
"kb": f"{DGIDB}:binder",
"kd": f"{DGIDB}:binder",
"kd1": f"RO:0002434",
"ka": f"RO:0002436",
"kact": f"RO:0002436", # is this a miss type of kcat?
"kb": f"RO:0002436", # {DGIDB}:binder maps to biolink:binds which is depreciated
"kd": f"RO:0002436",
"kd1": f"RO:0002436", # RO:0002434 maps to biolink:related_to
"ki": f"{DGIDB}:inhibitor",
"km": f"RO:0002434",
"ks": f"RO:0002434",
"km": f"RO:0002436",
"ks": f"RO:0002436",
"modulator": f"{DGIDB}:modulator",
"mic": f"RO:0002434",
"mpc": f"RO:0002434",
"mic": f"RO:0002434", # What is this referring to?
"mpc": f"RO:0002434", # What is this referring to?
"negative_modulator": f"{CHEMBL_MECHANISM}:negative_modulator",
"negative_allosteric_modulator": f"{CHEMBL_MECHANISM}:negative_modulator",
"opener": f"{CHEMBL_MECHANISM}:opener",
"other": f"{DGIDB}:other",
"partial_agonist": f"{DGIDB}:partial_agonist",
"pa2": f"RO:0002434",
"pa2": f"RO:0002434", # What is this referring to?
"pharmacological_chaperone": f"{DGIDB}:chaperone",
"positive_allosteric_modulator": f"{CHEMBL_MECHANISM}:positive_modulator",
"positive_modulator": f"{CHEMBL_MECHANISM}:positive_modulator",
"releasing_agent": f"{CHEMBL_MECHANISM}:releasing_agent",
"substrate": f"{CHEMBL_MECHANISM}:substrate",
"xc50": f"RO:0002434"
"xc50": f"RO:0002436" # This is related to ec50 and ic50 both of which describe binding events
}
10 changes: 5 additions & 5 deletions parsers/BINDING/src/loadBINDINGDB.py
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Expand Up @@ -52,7 +52,7 @@ class BINDINGDBLoader(SourceDataLoader):
source_data_url = "https://www.bindingdb.org/rwd/bind/chemsearch/marvin/SDFdownload.jsp?all_download=yes"
license = "All data and download files in bindingDB are freely available under a 'Creative Commons BY 3.0' license.'"
attribution = 'https://www.bindingdb.org/rwd/bind/info.jsp'
parsing_version = '1.5'
parsing_version = '1.6'

def __init__(self, test_mode: bool = False, source_data_dir: str = None):
"""
Expand All @@ -66,12 +66,12 @@ def __init__(self, test_mode: bool = False, source_data_dir: str = None):
self.affinity_threshold = LOG_SCALE_AFFINITY_THRESHOLD

self.measure_to_predicate = {
"pKi": "biolink:binds",
"pKi": "{DGIDB}:inhibitor", #inhibition constant
"pIC50": "CTD:decreases_activity_of",
"pKd": "biolink:binds",
"pKd": "RO:0002436",
"pEC50": "CTD:increases_activity_of",
"k_on": "biolink:binds",
"k_off": "biolink:binds"
"k_on": "RO:0002436",
"k_off": "RO:0002436"
}

self.bindingdb_version = None
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12 changes: 7 additions & 5 deletions parsers/PHAROS/src/loadPHAROS.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@ class PHAROSLoader(SourceDataLoader):
source_data_url = "https://pharos.nih.gov/"
license = "Data accessed from Pharos and TCRD is publicly available from the primary sources listed above. Please respect their individual licenses regarding proper use and redistribution."
attribution = 'Sheils, T., Mathias, S. et al, "TCRD and Pharos 2021: mining the human proteome for disease biology", Nucl. Acids Res., 2021. DOI: 10.1093/nar/gkaa993'
parsing_version: str = '1.6'
parsing_version: str = '1.7'

GENE_TO_DISEASE_QUERY: str = """select distinct x.value, d.did, d.name, p.sym, d.dtype, d.score
from disease d
Expand Down Expand Up @@ -63,16 +63,18 @@ class PHAROSLoader(SourceDataLoader):
}

# we might want more granularity here but for now it's one-to-one source with KL/AT
# we will need to develop a procedure for merging KL/AT moving forward
PHAROS_KL_AT_lookup = {
'CTD': (PREDICATION, MANUAL_AGENT),
'DisGeNET': (NOT_PROVIDED, NOT_PROVIDED),
'DrugCentral Indication': (KNOWLEDGE_ASSERTION, MANUAL_AGENT),
'eRAM': (NOT_PROVIDED, NOT_PROVIDED),
# For more information about JensenLab Databases: DOI: https://doi.org/10.1093/database/baac019
'JensenLab Experiment TIGA': (PREDICATION, AUTOMATED_AGENT),
'JensenLab Knowledge AmyCo': (NOT_PROVIDED, NOT_PROVIDED),
'JensenLab Knowledge MedlinePlus': (NOT_PROVIDED, NOT_PROVIDED),
'JensenLab Knowledge UniProtKB-KW': (NOT_PROVIDED, NOT_PROVIDED),
'JensenLab Text Mining': (NOT_PROVIDED, NOT_PROVIDED),
'JensenLab Knowledge AmyCo': (KNOWLEDGE_ASSERTION, MANUAL_AGENT),
'JensenLab Knowledge MedlinePlus': (KNOWLEDGE_ASSERTION, MANUAL_AGENT),
'JensenLab Knowledge UniProtKB-KW': (KNOWLEDGE_ASSERTION, MANUAL_VALIDATION_OF_AUTOMATED_AGENT),
'JensenLab Text Mining': (NOT_PROVIDED, TEXT_MINING_AGENT),
'Monarch': (NOT_PROVIDED, NOT_PROVIDED),
'UniProt Disease': (KNOWLEDGE_ASSERTION, MANUAL_AGENT)
}
Expand Down
2 changes: 1 addition & 1 deletion parsers/drugcentral/src/loaddrugcentral.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@ class DrugCentralLoader(SourceDataLoader):
source_data_url = "https://drugcentral.org/download"
license = "https://drugcentral.org/privacy"
attribution = "https://drugcentral.org/about"
parsing_version: str = '1.4'
parsing_version: str = '1.5'

omop_relationmap = {'off-label use': 'RO:0002606', # is substance that treats
'reduce risk': 'RO:0002606', # is substance that treats
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2 changes: 1 addition & 1 deletion parsers/gtopdb/src/loadGtoPdb.py
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Original file line number Diff line number Diff line change
Expand Up @@ -57,7 +57,7 @@ class GtoPdbLoader(SourceDataLoader):
source_data_url = "http://www.guidetopharmacology.org/"
license = "https://www.guidetopharmacology.org/about.jsp#license"
attribution = "https://www.guidetopharmacology.org/citing.jsp"
parsing_version: str = '1.3'
parsing_version: str = '1.4'

def __init__(self, test_mode: bool = False, source_data_dir: str = None):
"""
Expand Down

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