def analyseFile(splitFileID, relPMIDs):
fileID = "{:>4}".format(splitFileID).replace(" ", "0")
diseaseHitsFile = resultBase + "/disease/medline17n" + fileID + ".index"
hitsFile = SyngrepHitFile(diseaseHitsFile, diseaseMap)
if len(hitsFile) == 0:
return
print("Document: " + str(fileID))
print("Start Document: " + str(fileID))
procDB = neo4jInterface(simulate=False, printQueries=False)
for docID in hitsFile:
if not docID in relPMIDs:
continue
synHits = hitsFile.getHitsForDocument(docID)
foundUniqueHits = set()
for hit in synHits:
if len(hit.foundSyn) < 5:
if not hit.perfectHit:
continue
hitSyn = hit.synonym
foundUniqueHits.add(hitSyn.id.replace('_', ':'))
for synonymID in foundUniqueHits:
pubmedExists = False
if addUnknownPubmeds:
procDB.createNodeIfNotExists(['EVIDENCE', 'PUBMED'],
{'id': docID})
pubmedExists = True
else:
if procDB.nodeExists(['PUBMED'], {'id': docID}):
pubmedExists = True
if pubmedExists:
res = procDB.createRelationship('disease', ['DISEASE'],
{'id': synonymID}, 'pubmed',
['PUBMED'], {'id': docID},
['DISEASE_MENTION'], None)
print("Add: ", fileID, docID, synonymID,
[x for x in res if res != None])
print("End Document: " + str(fileID))
procDB.close()
def analyseFile(splitFileIDs, env):
fileCoocs = []
for splitFileID in splitFileIDs:
diseaseFile = resultBase + "/disease/" + splitFileID + ".index"
diseaseHits = SyngrepHitFile(diseaseFile, diseaseSyns)
if len(diseaseHits) == 0:
continue
sentFile = "/mnt/c/dev/data/pmc/allsent/" + splitFileID + ".sent"
sentDB = SentenceDB(sentFile)
sys.stderr.write("Found something in: " + str(splitFileID) + "\n")
for docID in diseaseHits:
docHits = diseaseHits.getHitsForDocument(docID)
allSynIDs = set()
for hit in docHits:
allSynIDs.add(hit.synonym.id.replace('_', ':', 1))
removeIDs = set()
for synID in allSynIDs:
gterm = celloObo.getID(synID)
allChildren = gterm.getAllChildren(maxLevel=2)
for x in allChildren:
removeIDs.add(x)
allowedIDs = [x for x in allSynIDs if not x in removeIDs]
#allowedIDs = allSynIDs.remove(removeIDs)
allterms = []
for synID in allowedIDs:
gterm = celloObo.getID(synID)
allterms.append(gterm)
fileCoocs.append((docID, gterm.id, gterm.name))
sys.stderr.write("Found {cnt} elems in files {ids}\n".format(
cnt=str(len(fileCoocs)), ids=str(splitFileIDs)))
printed = printStuff(None, fileCoocs, None)
sys.stderr.write(
"Found {cnt} (printed: {printed}) elems in files {ids}\n".format(
cnt=str(len(fileCoocs)), ids=str(splitFileIDs), printed=printed))
return None
def analyseFile(splitFileIDs, env):
subject2pmids = defaultdict(set)
for splitFileID in splitFileIDs:
fileID = "{:>4}".format(splitFileID).replace(" ", "0")
fmaFile = resultBase + "/model_anatomy/pubmed18n" + fileID + ".index"
doidFile = resultBase + "/disease/pubmed18n" + fileID + ".index"
goFile = resultBase + "/neutrophils/pubmed18n" + fileID + ".index"
sentFile = "/mnt/c/dev/data/pubmed/pubmed18n" + fileID + ".sent"
fmaHits = SyngrepHitFile(fmaFile, fmaSyns)
if len(fmaHits) == 0:
return
print("Processing file: ", fileID)
doidHits = SyngrepHitFile(doidFile, doidSyns)
goHits = SyngrepHitFile(goFile, goSyns)
sentDB = SentenceDB(sentFile)
for docID in fmaHits:
docFMAHits = fmaHits.getHitsForDocument(docID)
docDoidHits = doidHits.getHitsForDocument(docID)
docGOHits = goHits.getHitsForDocument(docID)
# no tissue hits at all ...
if len(docFMAHits) == 0:
continue
# is neutrophil hit? if no -> continue
neutrophilMentioned = testMentioned(docFMAHits, neutrophilSynIDs)
if not neutrophilMentioned:
continue
subject2pmids['NEUTROPHIL'].add(int(docID))
if testMentioned(docFMAHits, tissueIDs):
subject2pmids['TISSUES'].add(int(docID))
if testMentioned(docDoidHits, doidSynIDs):
subject2pmids['DOID'].add(int(docID))
if testMentioned(docGOHits, goSynIDs):
subject2pmids['INFLAMM'].add(int(docID))
return subject2pmids
def analyseFile(splitFileIDs, env):
fileCoocs = []
for splitFileID in splitFileIDs:
ent1File = resultBase + "/"+args.folder1+"/" + splitFileID + ".index"
ent2File = resultBase + "/"+args.folder2+"/" + splitFileID + ".index"
relFile = resultBase + "/relations/" + splitFileID + ".index"
sentFile = args.sentdir + "/" + splitFileID + ".sent"
ent1Hits = SyngrepHitFile(ent1File, ent1Syns)
if len(ent1Hits) == 0:
continue
ent2Hits = SyngrepHitFile(ent2File, ent2Syns)
if len(ent2Hits) == 0:
continue
relHits = SyngrepHitFile(relFile, relSyns)
# only load sentences if there's a hit ...
sentDB = None
sys.stderr.write("Found something in: " + str(splitFileID) + "\n")
for docID in ent1Hits:
if docID in ent2Hits:
if sentDB == None:
sentDB = SentenceDB(sentFile)
ent1SynHits = ent1Hits.getHitsForDocument(docID)
ent2SynHits = ent2Hits.getHitsForDocument(docID)
# if docID == 'a27229723':
# [print(x.synonyme) for x in hgncSynHits]
# [print(x.synonyme) for x in mirnaSynHits]
foundCoocs = findCooccurrences(str(docID), ent1SynHits, ent2SynHits, sentDB, relHits)
fileCoocs += foundCoocs
sys.stderr.write("Found {cnt} elems in files {ids}\n".format(cnt=str(len(fileCoocs)), ids=str(splitFileIDs)))
printed = printStuff(None, fileCoocs, None)
thisProcID = str(os.getpid())
sys.stderr.write("{procID}: Found {cnt} (printed: {printed}) elems in files {ids}\n".format(
cnt=str(len(fileCoocs)),
ids=str(splitFileIDs),
printed=printed,
procID=thisProcID))
return None
def analyseFile(splitFileIDs, env):
fileCoocs = []
for splitFileID in splitFileIDs:
hgncFile = resultBase + "/hgnc/" + splitFileID + ".index"
mirnaFile = resultBase + "/mirna/" + splitFileID + ".index"
relFile = resultBase + "/relations/" + splitFileID + ".index"
sentFile = "/mnt/c/dev/data/pmc/allsent/" + splitFileID + ".sent"
mirnaHits = SyngrepHitFile(mirnaFile, mirnaSyns)
if len(mirnaHits) == 0:
continue
hgncHits = SyngrepHitFile(hgncFile, hgncSyns)
if len(hgncHits) == 0:
continue
relHits = SyngrepHitFile(relFile, relSyns)
sentDB = SentenceDB(sentFile)
sys.stderr.write("Found something in: " + str(splitFileID) + "\n")
for docID in mirnaHits:
if docID in hgncHits:
mirnaSynHits = mirnaHits.getHitsForDocument(docID)
hgncSynHits = hgncHits.getHitsForDocument(docID)
#if docID == 'a27229723':
# [print(x.synonyme) for x in hgncSynHits]
# [print(x.synonyme) for x in mirnaSynHits]
foundCoocs = findCooccurrences(str(docID), hgncSynHits,
mirnaSynHits, sentDB, relHits)
fileCoocs += foundCoocs
sys.stderr.write("Found {cnt} elems in files {ids}\n".format(
cnt=str(len(fileCoocs)), ids=str(splitFileIDs)))
printed = printStuff(None, fileCoocs, None)
sys.stderr.write(
"Found {cnt} (printed: {printed}) elems in files {ids}\n".format(
cnt=str(len(fileCoocs)), ids=str(splitFileIDs), printed=printed))
return None
resultBase = dataDir + "/miRExplore/textmine/results/"
indexFoundSyns = Counter()
excludedSyns = loadExludeWords()
checkResultsFor = 'disease'
analyseFiles = 100
maxFiles = 892
checkSynsMap = SynfileMap(resultBase + "/" + checkResultsFor + "/synfile.map")
checkSynsMap.loadSynFiles(('/home/users/joppich/ownCloud/data/', dataDir))
for splitFileID in range(maxFiles, maxFiles - analyseFiles - 1, -1):
fileID = "{:>4}".format(splitFileID).replace(" ", "0")
print(fileID)
indexFile = resultBase + "/" + checkResultsFor + "/medline17n" + fileID + ".index"
foundHits = SyngrepHitFile(indexFile, checkSynsMap)
for doc in foundHits:
docHits = foundHits.getHitsForDocument(doc)
for hit in docHits:
indexFoundSyns[hit.hitSyn] += 1
for (syn, cnt) in indexFoundSyns.most_common(100):
#if syn in excludedSyns:
print(str(syn) + " -> " + str(cnt))
def analyseFile(splitFileIDs, env):
fileCoocs = []
for splitFileID in splitFileIDs:
diseaseFile = resultBase + "/model_anatomy/" + splitFileID + ".index"
diseaseHits = SyngrepHitFile(diseaseFile, diseaseSyns)
if len(diseaseHits) == 0:
continue
sentFile = args.sentdir + "/" + splitFileID + ".sent" #"/mnt/c/dev/data/pmc/allsent/"+splitFileID +".sent"
sentDB = SentenceDB(sentFile)
sys.stderr.write("Found something in: " + str(splitFileID) + "\n")
for docID in diseaseHits:
docHits = diseaseHits.getHitsForDocument(docID)
synid2loc = defaultdict(list)
allSynIDs = set()
for hit in docHits:
if "and " in hit.foundSyn:
continue
allSynIDs.add(hit.synonym.id)
synid2loc[hit.synonym.id].append(
(str(hit.documentID), hit.position[0],
hit.position[1]))
removeIDs = set()
for synID in allSynIDs:
gterm = getTerm(synID, fmaObo)
if gterm == None:
sys.stderr.write("Invalid synID: " + synID)
removeIDs.add(synID)
continue
allChildren = gterm.getAllChildren(maxLevel=2)
for x in allChildren:
removeIDs.add(x)
allowedIDs = [x for x in allSynIDs if not x in removeIDs]
#allowedIDs = allSynIDs.remove(removeIDs)
allterms = []
for synID in allowedIDs:
gterm = getTerm(synID, fmaObo)
allterms.append(gterm)
fileCoocs.append(
(docID, gterm.id, gterm.name, synid2loc[synID]))
sys.stderr.write("Found {cnt} elems in files {ids}\n".format(
cnt=str(len(fileCoocs)), ids=str(splitFileIDs)))
printed = printStuff(None, fileCoocs, None)
sys.stderr.write(
"Found {cnt} (printed: {printed}) elems in files {ids}\n".format(
cnt=str(len(fileCoocs)),
ids=str(splitFileIDs),
printed=printed))
return None
def analyseFile(splitFileIDs, env):
fileCoocs = []
for splitFileID in splitFileIDs:
fileID = "{:>4}".format(splitFileID).replace(" ", "0")
hgncFile = resultBase + "/hgnc/pubmed18n" + fileID + ".index"
mirnaFile = resultBase + "/mirna/pubmed18n" + fileID + ".index"
sentFile = "/mnt/c/dev/data/pubmed/pubmed18n" + fileID + ".sent"
mirnaHits = SyngrepHitFile(mirnaFile, mirnaSyns)
if len(mirnaHits) == 0:
continue
hgncHits = SyngrepHitFile(hgncFile, hgncSyns)
if len(hgncHits) == 0:
continue
sentDB = SentenceDB(sentFile)
sys.stderr.write("Found something in: " + str(fileID) + "\n")
for docID in mirnaHits:
if docID in hgncHits:
mirnaSynHits = mirnaHits.getHitsForDocument(docID)
hgncSynHits = hgncHits.getHitsForDocument(docID)
#if docID == 'a27229723':
# [print(x.synonyme) for x in hgncSynHits]
# [print(x.synonyme) for x in mirnaSynHits]
foundCoocs = findCooccurrences(str(docID), hgncSynHits,
mirnaSynHits, sentDB)
fileCoocs += foundCoocs
assocByGene = defaultdict(set)
for x in foundCoocs:
geneID = x.gene
geneLabel = 'GENE'
mirnaID = x.mirna
mirnaLabel = x.idtype
assoc = (geneID, geneLabel, mirnaID, mirnaLabel)
assocByGene[assoc[0]].add(assoc)
addDocAsEvidence = False
assocByTypeForGene = {}
for gene in assocByGene:
assocs = assocByGene[gene]
mimatSet = set()
miSet = set()
orgmirSet = set()
familySet = set()
for assoc in assocs:
if assoc[3] == 'MIRNA':
mimatSet.add(assoc)
elif assoc[3] == 'MIRNA_PRE':
miSet.add(assoc)
elif assoc[3] == 'MIRNA_ORGMIR':
orgmirSet.add(assoc)
elif assoc[3] == 'MIRNA_FAMILY':
familySet.add(assoc)
else:
print("Unknown relation in doc: " + docID)
print(assoc)
if len(mimatSet) > 0 or len(miSet) > 0 or len(
orgmirSet) > 0 or len(familySet) > 0:
assocByTypeForGene[gene] = (mimatSet, miSet, orgmirSet,
familySet)
#filter assocs here such that if a taxid specific version was found, not the general version is added
if len(assocByTypeForGene) > 0:
if db:
db.createNodeIfNotExists(['EVIDENCE', 'PUBMED'],
{'id': docID})
print("Adding: " + str(docID) + ": " +
str(assocByTypeForGene))
#
# TODO first create all unique edges
# TODO add genes to mirna edges and mirnas to gene edges to keep track from where an edge originates
# TODO edges should get weights = how many relations have been found
#
mirnaEdges = defaultdict(set)
geneEdges = defaultdict(set)
for gene in assocByTypeForGene:
assocsForGene = assocByTypeForGene[
gene] # (mimatSet, miSet, orgmirSet, familySet)
for subSet in assocsForGene:
for cooc in subSet:
geneEdges[(cooc[0], cooc[1])].add(
(cooc[2], cooc[3]))
mirnaEdges[(cooc[2], cooc[3])].add(
(cooc[0], cooc[1]))
for edge in geneEdges:
edgeMirnas = [x[0] for x in geneEdges[edge]]
if db:
db.createRelationship('gene', [edge[1]],
{'id': edge[0]}, 'pmid',
['PUBMED'], {'id': docID},
['ST_MENTION'], {
'type': 'GENE_MENTION',
'mirnas': edgeMirnas
})
for edge in mirnaEdges:
edgeGenes = [x[0] for x in mirnaEdges[edge]]
if db:
db.createRelationship('pmid', ['PUBMED'],
{'id': docID}, 'mi',
[edge[1]], {'id': edge[0]},
['ST_MENTION'], {
'type': 'MIRNA_MENTION',
'genes': edgeGenes
})
sys.stderr.write("Found {cnt} elems in files {ids}\n".format(
cnt=str(len(fileCoocs)), ids=str(splitFileIDs)))
printed = printStuff(None, fileCoocs, None)
sys.stderr.write(
"Found {cnt} (printed: {printed}) elems in files {ids}\n".format(
cnt=str(len(fileCoocs)), ids=str(splitFileIDs), printed=printed))
return None
def analyseFile(splitFileID, relPMIDs):
fileID = "{:>4}".format(splitFileID).replace(" ", "0")
diseaseHitsFile = resultBase + "/cellline/medline17n" + fileID + ".index"
hitsFile = SyngrepHitFile(diseaseHitsFile, celllinesMap)
if len(hitsFile) == 0:
return
print("Start Document: " + str(fileID))
procDB = neo4jInterface(simulate=False, printQueries=False)
for docID in hitsFile:
if not docID in relPMIDs:
continue
synHits = hitsFile.getHitsForDocument(docID)
foundUniqueHits = set()
foundOrgs = set()
for hit in synHits:
if len(hit.foundSyn) < 5:
if not hit.perfectHit:
continue
hitSynFileID = hit.synonymID.synfile
foundOrgs.add(synfileID2tax[hitSynFileID])
hitSyn = hit.synonym
foundUniqueHits.add(hitSyn.id)
if len(foundUniqueHits) == 0:
continue
for celllineID in foundUniqueHits:
pubmedExists = False
if addUnknownPubmeds:
procDB.createNodeIfNotExists(['EVIDENCE', 'PUBMED'],
{'id': docID})
pubmedExists = True
else:
if procDB.nodeExists(['PUBMED'], {'id': docID}):
pubmedExists = True
if pubmedExists:
res = procDB.createRelationship('cellline', ['CELLLINE'],
{'id': celllineID}, 'pubmed',
['PUBMED'], {'id': docID},
['CELLLINE_MENTION'], None)
print("Add: ", fileID, docID, celllineID,
[x for x in res if res != None])
foundOrgs = foundOrgs.difference(allSet)
if len(foundOrgs) == 1:
pass
# create relation
# print('Associate: ' + str(foundOrgs))
elif len(foundOrgs) == 0:
pass
elif len(foundOrgs) > 1:
# print('Ambiguous pubmed: ' + docID)
pass
print("End Document: " + str(fileID))
procDB.close()
def analyseFile(splitFileIDs, env):
fileCoocs = []
for splitFileID in splitFileIDs:
print(splitFileID, file=sys.stderr)
ent1File = resultBase + "/" + args.folder1 + "/" + splitFileID + ".index"
ent2File = resultBase + "/" + args.folder2 + "/" + splitFileID + ".index"
relFile = resultBase + "/relations/" + splitFileID + ".index"
sentFile = args.sentdir + "/" + splitFileID + ".sent"
ent1Hits = SyngrepHitFile(ent1File,
ent1Syns,
sentIDNoText=args.sentid_no_text)
if len(ent1Hits) == 0:
continue
ent2Hits = SyngrepHitFile(ent2File,
ent2Syns,
sentIDNoText=args.sentid_no_text)
if len(ent2Hits) == 0:
continue
relHits = SyngrepHitFile(relFile,
relSyns,
sentIDNoText=args.sentid_no_text)
# only load sentences if there's a hit ...
sentDB = None
sys.stderr.write("Found something in: " + str(splitFileID) + "\n")
for docID in ent1Hits:
#if not docID in ["27150436"]:
# continue
if accept_pmids != None:
if not docID in accept_pmids:
continue
if docID in ent2Hits:
if sentDB == None:
sentDB = SentenceDB(sentFile,
sent_no_byte=args.sent_no_byte)
ent1SynHits = ent1Hits.getHitsForDocument(docID)
ent2SynHits = ent2Hits.getHitsForDocument(docID)
# if docID == 'a27229723':
# [print(x.synonyme) for x in hgncSynHits]
# [print(x.synonyme) for x in mirnaSynHits]
foundCoocs = findCooccurrences(str(docID), ent1SynHits,
ent2SynHits, sentDB, relHits)
for relEntEnt in foundCoocs:
if relEntEnt.accepted():
print(str(relEntEnt), flush=True)
"""
print(
"{ent1}\t{ent1found}\t{ent1type}\t{ent2}\t{ent2found}\t{ent2type}\t{pubmed}\t{sapar}\t{sase}\t{relation}\n".format(
ent1=cooc.ent1,
ent2=cooc.ent2,
ent1found=cooc.ent1found,
ent2found=cooc.ent2found,
ent1type=cooc.ent1type,
ent2type=cooc.ent2type,
pubmed=cooc.pubmed,
sapar=cooc.sameParagraph,
sase=cooc.sameSentence,
relation=cooc.relation,
), end='', flush=True)
"""
fileCoocs += foundCoocs
sys.stderr.write("Found {cnt} elems in files {ids}\n".format(
cnt=str(len(fileCoocs)), ids=str(splitFileIDs)))
#printed = printStuff(None, fileCoocs, None)
thisProcID = str(os.getpid())
sys.stderr.write(
"{procID}: Found {cnt} (printed: {printed}) elems in files {ids}\n".
format(cnt=str(len(fileCoocs)),
ids=str(splitFileIDs),
printed=len(fileCoocs),
procID=thisProcID))
return None
def analyseFile(splitFileIDs, env):
fileCoocs = []
for splitFileID in splitFileIDs:
diseaseFile = resultBase + "/org/" + splitFileID + ".index"
diseaseHits = SyngrepHitFile(diseaseFile, diseaseSyns)
if len(diseaseHits) == 0:
continue
sentFile = args.sentdir + "/" + splitFileID + ".sent" #"/mnt/c/dev/data/pmc/allsent/"+splitFileID +".sent"
sentDB = SentenceDB(sentFile)
sys.stderr.write("Found something in: " + str(splitFileID) + "\n")
for docID in diseaseHits:
docHits = diseaseHits.getHitsForDocument(docID)
synid2loc = defaultdict(list)
allSynIDs = set()
for hit in docHits:
if "and " in hit.foundSyn:
continue
allSynIDs.add(hit.synonym.id)
synid2loc[hit.synonym.id].append(
(str(hit.documentID), hit.position[0],
hit.position[1]))
#allowedIDs = allSynIDs.remove(removeIDs)
allowedOrgIDs = []
evs = []
for x in synid2loc:
if orgID2TLC.get(x, None) != None:
allowedOrgIDs.append(x)
evs += synid2loc[x]
fileCoocs.append(
(docID, ",".join([orgID2TLC[x]
for x in allowedOrgIDs]), evs))
sys.stderr.write("Found {cnt} elems in files {ids}\n".format(
cnt=str(len(fileCoocs)), ids=str(splitFileIDs)))
printed = printStuff(None, fileCoocs, None)
sys.stderr.write(
"Found {cnt} (printed: {printed}) elems in files {ids}\n".format(
cnt=str(len(fileCoocs)),
ids=str(splitFileIDs),
printed=printed))
return None
def analyseFile(splitFileIDs, env):
fileCoocs = []
for splitFileID in splitFileIDs:
indexFile = resultBase + "/" + splitFileID + ".index"
oboHits = SyngrepHitFile(indexFile,
oboSyns,
sentIDNoText=args.sentid_no_text)
if len(oboHits) == 0:
continue
# not used anyhow ...
#sentFile = args.sentdir + "/" + splitFileID + ".sent"
#sentDB = SentenceDB(sentFile)
sys.stderr.write("Found something in: " + str(splitFileID) + "\n")
for docID in oboHits:
if accept_pmids != None:
if not docID in accept_pmids:
continue
docHits = oboHits.getHitsForDocument(docID)
synid2loc = defaultdict(list)
allSynIDs = set()
for hit in docHits:
if len(hit.foundSyn) < args.phit:
if hit.perfectHit != True:
continue
if "and " in hit.foundSyn:
continue
if hit.synonym is None:
print(hit, file=sys.stderr)
sys.stderr.flush()
allSynIDs.add(hit.synonym.id)
synid2loc[hit.synonym.id].append(
(str(hit.documentID), hit.position[0], hit.position[1],
hit.hitSyn))
removeIDs = set()
for synID in allSynIDs:
gterm = getTerm(synID, celloObo)
if gterm == None:
sys.stderr.write("Invalid synID: " + synID)
removeIDs.add(synID)
continue
allChildren = gterm.getAllChildren(maxLevel=2)
for x in allChildren:
removeIDs.add(x)
allowedIDs = [x for x in allSynIDs if not x in removeIDs]
#allowedIDs = allSynIDs.remove(removeIDs)
allterms = []
for synID in allowedIDs:
gterm = getTerm(synID, celloObo)
allterms.append(gterm)
fileCoocs.append(
(docID, gterm.id, gterm.name, synid2loc[synID]))
sys.stderr.write("Found {cnt} elems in files {ids}\n".format(
cnt=str(len(fileCoocs)), ids=str(splitFileIDs)))
printed = printStuff(None, fileCoocs, None)
sys.stderr.write(
"Found {cnt} (printed: {printed}) elems in files {ids}\n".format(
cnt=str(len(fileCoocs)),
ids=str(splitFileIDs),
printed=printed))
return None
