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SciDataLib-79 Code does not recognize ontological value
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reworked the code to implement this (but not yet at all levels)
- updated __addid
- added __chkont function to update the key of name/value pair with trailing '#' if not already present
- updated examples
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@stuchalk
stuchalk committed Dec 18, 2023
1 parent b54fc51 commit f2f09e3
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Showing 4 changed files with 110 additions and 46 deletions.
12 changes: 8 additions & 4 deletions examples/example.py
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Original file line number Diff line number Diff line change
Expand Up @@ -41,10 +41,14 @@ def create_scidata():
link = 'https://stuchalk.github.io/scidata/examples/ph_min.jsonld'
example.permalink(link)

# add discipline and subdiscipline (plus namespace)
# add namespaces (needed for values that point to ontological definitions of things)
example.namespaces({'w3i': 'https://w3id.org/skgo/modsci#'})
example.discipline('w3i:Chemistry')
example.subdiscipline('w3i:ChemicalInformatics')
example.namespaces({'qudt': 'https://qudt.org/vocab/unit/'})
example.namespaces({'obo': 'http://purl.obolibrary.org/obo/'})

# add discipline and subdiscipline
example.discipline('Chemistry')
example.subdiscipline('w3i:Cheminformatics')

""" METHODOLOGY SECTION """
# methodology data goes into the aspects array in the JSON-LD file
Expand Down Expand Up @@ -363,7 +367,7 @@ def create_scidata():
"type": "IC50",
"value":
"12.300000000000000000000000000000",
"units": "uM"}]}]}]
"units": "qudt:MicroM"}]}]}]

example.scidatapackage(packet)

Expand Down
58 changes: 29 additions & 29 deletions examples/example3.py
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Original file line number Diff line number Diff line change
Expand Up @@ -38,54 +38,54 @@
'chebi': 'obo:CHEBI_15377'}

con1 = {
'@id': 'constituent',
'@id': 'constituent/1/',
'source': 'substance/1/',
'role': 'chm:analyte',
'properties': [{
'@id': 'property',
'quantity': 'mass of substance per volume',
'property': 'Concentration (w/v)',
'quantities': [{
'@id': 'quantity/1/',
'quantitykind': 'mass of substance per volume',
'quantity': 'Concentration (w/v)',
'value': {
'@id': 'value', 'number': 2.99, 'unitref': 'qudt:PPM'}
}, {
'@id': 'property',
'quantity': 'volume',
'property': 'Volume of solution',
'@id': 'quantity/2/',
'quantitykind': 'volume',
'quantity': 'Volume of solution',
'value': {
'@id': 'value', 'number': 100.0, 'unitref': 'qudt:MilliL'}
}]
}
con2 = {
'@id': 'constituent',
'@id': 'constituent/2/',
'source': 'substance/2/',
'role': 'chm:reagent',
'properties': [{
'@id': 'property',
'quantity': 'mass of substance per volume',
'property': 'Concentration (w/v)',
'@id': 'quantity/1/',
'quantitykind': 'mass of substance per volume',
'quantity': 'Concentration (w/v)',
'value': {
'@id': 'value', 'number': 2.99, 'unitref': 'qudt:PPM'}
}, {
'@id': 'property',
'quantity': 'volume',
'property': 'Volume of solution',
'@id': 'quantity/2/',
'quantitykind': 'volume',
'quantity': 'Volume of solution',
'value': {
'@id': 'value', 'number': 100.0, 'unitref': 'qudt:MilliL'}
}]}
con3 = {
'@id': 'constituent',
'@id': 'constituent/3/',
'source': 'substance/3/',
'role': 'chm:reagent'}
con4 = {
'@id': 'constituent',
'@id': 'constituent/4/',
'source': 'substance/4/',
'role': 'chm:buffer'}
con5 = {
'@id': 'constituent',
'@id': 'constituent/5/',
'source': 'substance/5/',
'role': 'chm:solvent'}
con6 = {
'@id': 'constituent',
'@id': 'constituent/6/',
'source': 'substance/6/',
'role': 'chm:solvent'}
cons = [con1, con2, con3, con4, con5, con6]
Expand All @@ -99,25 +99,25 @@
'phase#': 'sub:liquid',
'constituents': cons,
'properties': [{
'@id': 'property',
'quantity': 'mass of substance per volume',
'property': 'Concentration (w/v)',
'@id': 'quantity/1/',
'quantitykind': 'mass of substance per volume',
'quantity': 'Concentration (w/v)',
'value': {
'@id': 'value', 'number': 4, 'unitref': 'qudt:PPM'}
}, {
'@id': 'property',
'quantity': 'volume',
'property': 'Volume of solution',
'@id': 'quantity/2/',
'quantitykind': 'volume',
'quantity': 'Volume of solution',
'value': {
'@id': 'value', 'number': 250.0, 'unitref': 'qudt:MilliL'}
}]}
con1 = {
'@id': 'condition',
'@id': 'condition/1/',
'source': 'measurement/1/',
'scope': 'substance/1/',
'quantity': 'temperature',
'property': 'Ambient temperature',
'propertyref': 'gb:T06321',
'quantitykind': 'temperature',
'quantity': 'Ambient temperature',
'quantity#': 'gb:T06321',
'value': '100.0'}
facets = [comp1, comp2, comp3, comp4, comp5, comp6, sub1, con1]
example.facets(facets)
Expand Down
20 changes: 20 additions & 0 deletions examples/testnum.py
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Original file line number Diff line number Diff line change
@@ -0,0 +1,20 @@
""" testing functions """
from scidatalib.scidata import SciData
import json


def scidata_nums():
uid = 'ids'
testy = SciData(uid)
# add discipline and subdiscipline data
src = {
'citation': 'Example SciData JSON-LD file, Chalk Research Group',
'url': 'https://stuchalk.github.io/scidata/examples/ph_min.jsonld',
'stype': 'dataset',
'otype#': 'sdo:dataset'
}
testy.sources([src])
print(json.dumps(testy.output, indent=4, ensure_ascii=False))


scidata_nums()
66 changes: 53 additions & 13 deletions scidatalib/scidata.py
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Original file line number Diff line number Diff line change
Expand Up @@ -46,11 +46,14 @@ def __init__(self, uid: str):
"@id": "scidata/",
"@type": "sdo:scientificData",
"discipline": "", # def discipline
"discipline#": "", # def discipline (ont entry)
"subdiscipline": "", # def subdiscipline
"subdiscipline#": "", # def subdiscipline (ont entry)
"methodology": {
"@id": "methodology/",
"@type": "sdo:methodology",
"evaluation": "", # def evaluation
"evaluation#": "", # def evaluation (ont entry)
"aspects": []}, # def aspects OR def scidatapacket
"system": {
"@id": "system/",
Expand Down Expand Up @@ -490,9 +493,15 @@ def discipline(self, disc: str) -> str:
"""
if isinstance(disc, str):
if ":" in disc:
self.__addid(disc)
self.meta['@graph']['scidata']['discipline'] = disc
return self.meta['@graph']['scidata']['discipline']
if self.__addid(disc):
self.meta['@graph']['scidata']['discipline#'] = disc
return self.meta['@graph']['scidata']['discipline#']
else:
self.meta['@graph']['scidata']['discipline'] = disc
return self.meta['@graph']['scidata']['discipline']
else:
self.meta['@graph']['scidata']['discipline'] = disc
return self.meta['@graph']['scidata']['discipline']

def subdiscipline(self, subdisc: str) -> str:
"""
Expand All @@ -511,9 +520,15 @@ def subdiscipline(self, subdisc: str) -> str:
"""
if isinstance(subdisc, str):
if ":" in subdisc:
self.__addid(subdisc)
self.meta['@graph']['scidata']['subdiscipline'] = subdisc
return self.meta['@graph']['scidata']['subdiscipline']
if self.__addid(subdisc):
self.meta['@graph']['scidata']['subdiscipline#'] = subdisc
return self.meta['@graph']['scidata']['subdiscipline#']
else:
self.meta['@graph']['scidata']['subdiscipline'] = subdisc
return self.meta['@graph']['scidata']['subdiscipline']
else:
self.meta['@graph']['scidata']['subdiscipline'] = subdisc
return self.meta['@graph']['scidata']['subdiscipline']

def evaluation(self, evaln: str) -> str:
"""
Expand All @@ -532,9 +547,15 @@ def evaluation(self, evaln: str) -> str:
"""
if isinstance(evaln, str):
if ":" in evaln:
self.__addid(evaln)
self.meta['@graph']['scidata']['methodology']['evaluation'] = evaln
return self.meta['@graph']['scidata']['methodology']['evaluation']
if self.__addid(evaln):
self.meta['@graph']['scidata']['methodology']['evaluation#'] = evaln
return self.meta['@graph']['scidata']['methodology']['evaluation#']
else:
self.meta['@graph']['scidata']['methodology']['evaluation'] = evaln
return self.meta['@graph']['scidata']['methodology']['evaluation']
else:
self.meta['@graph']['scidata']['methodology']['evaluation'] = evaln
return self.meta['@graph']['scidata']['methodology']['evaluation']

def aspects(self, aspects: list) -> list:
"""Add to or replace the aspects of the file
Expand Down Expand Up @@ -883,7 +904,7 @@ def scidatapackage(self, package):
dp.update({'aspects#': ataspect})
self.datapoint(packet['dataset'])

def sources(self, sources: list, replace=False) -> dict:
def sources(self, sources: list, replace=False) -> list:
"""
Add to or replace the source reference list
Expand Down Expand Up @@ -913,6 +934,9 @@ def sources(self, sources: list, replace=False) -> dict:
'@id': 'source/' + str(len(srcs) + 1) + '/',
'@type': 'dc:source'
}
# check data in source for values that are ontological (':')
# updates dictionary keys with additional '#' if not present and needed
x = self.__chkont(x)
ld.update(x)
srcs.append(ld)
self.meta['@graph']['sources'] = srcs
Expand Down Expand Up @@ -949,14 +973,30 @@ def __addid(self, text: str) -> bool:
if isinstance(text, str):
if '://' in text:
return False
elif len(text.split(':')) > 1:
return False
elif ':' in text:
elif ':' in text and len(text.split(':')) == 2:
self.ids(text)
return True
else:
return False
else:
return False

def __chkont(self, data: dict) -> bool:
# checks that
keys = list(data.keys())
vals = list(data.values())
data = {}
for val in vals:
idx = vals.index(val)
if ':' in val:
# check this is ontology entry and if it is then check the dictionary key for '#'
if self.__addid(val):
# update dictionary name (keys) with '#' ending if not already present
if keys[idx][-1] != "#":
keys[idx] = keys[idx] + "#"
data.update({keys[idx]: vals[idx]})
return data

def __graphid(self, gid: str) -> bool:
"""
Assigns the @id value within the @graph JSON object.
Expand Down

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