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Pull latest from biomodels; update scripts for newly-revealed problems.
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Don't include new 1075, since it's not an SBML model, and because the file sizes in it are too large for github.
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@luciansmith
luciansmith committed Jun 1, 2024
1 parent 5f088be commit 24b8ecb
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Showing 3,462 changed files with 289,213 additions and 49,665 deletions.
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5 changes: 5 additions & 0 deletions create_metadata_rdf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -49,8 +49,10 @@ def get_uri(self):
"BIOMD0000000456" : NonStandardRef('Smallbone, Kieran. "Metabolic Control Analysis: Rereading Reder." arXiv preprint arXiv:1305.6449 (2013).', "http://arxiv.org/pdf/1305.6449v1.pdf", "Metabolic Control Analysis: Rereading Reder."),
"BIOMD0000000882" : NonStandardRef('Munz, Philip, et al. "When zombies attack!: mathematical modelling of an outbreak of zombie infection." Infectious disease modelling research progress 4 (2009): 133-150.', "http://identifiers.org/isbn/ISBN:1607413477", "When zombies attack!: Mathematical modelling of an outbreak of zombie infection"),
"BIOMD0000001045" : NonStandardRef('Smith, David, and Lang Moore. "The SIR model for spread of disease-the differential equation model." Convergence (2004).', "https://www.maa.org/press/periodicals/loci/joma/the-sir-model-for-spread-of-disease-the-differential-equation-model", "The SIR Model for Spread of Disease - The Differential Equation Model"),
"BIOMD0000001070" : NonStandardRef('Kong, Xiangzhe, Huang, Wenbing, and Yang Liu. "Conditional Antibody Design as 3D Equivariant Graph Translation.", arXiv preprint arXiv:2208.06073 (2022).', "http://identifiers.org/doi/10.48550/arXiv.2208.06073", "Conditional Antibody Design as 3D Equivariant Graph Translation."),
}


def parseDocAndAddToMetadata(filename, metadata, master, pubmedIDs, doiIDs):
doc = libsbml.readSBMLFromFile(filename)
model = doc.getModel()
Expand Down Expand Up @@ -89,6 +91,9 @@ def addCitationsToMetadata(pubmedIDs, doiIDs, masterID, metadata, id, temp_entry
mastercitation = get_reference(doi=doivec[-1])
else:
mastercitation = no_pubmed_or_doi[id]
if not mastercitation:
mastercitation = no_pubmed_or_doi[id]


for pmid in pubmedIDs:
citation = get_reference(pubmed_id=pmid)
Expand Down
45 changes: 25 additions & 20 deletions fix_sbml_validity.py
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Original file line number Diff line number Diff line change
Expand Up @@ -264,6 +264,7 @@ def fixIdentifiersNS(file, oldns, id):
"uniprot/GO:0005893": "go/GO:0005893",
"uniprot/PR:000050007": "pr/PR:000050007",
"unists/P00734": "uniprot/P00734",
"org/GO:": "org/go/GO:",
}

def fixURI(uri):
Expand All @@ -285,6 +286,8 @@ def retestAllIdentifiersURIs(file):
if "identifiers.org" in word:
for charstr in word.split('"'):
if "identifiers.org" in charstr:
if "org/GO:" in charstr:
bad_uris.append((file, charstr, "Missing 'go/'"))
# if "omim" in charstr:
# continue
# if "psimi" in charstr:
Expand Down Expand Up @@ -377,28 +380,30 @@ def run(id, sbml_files):
for charstr in word.split('"'):
if "identifiers.org" in charstr:
charvec = charstr.strip("'>/").split("/")
# print(charvec)
for n in range(len(charvec)):
if charvec[n] == "identifiers.org":
pmid = charvec[n+2]
if charvec[n+1] not in VALID_IDENTIFIERS_NAMESPACES:
# if checkAndAddIdentifiersNamespace(charvec[n+1]):
bad_identifiers_ns.add(charvec[n+1])
assert charvec[n-1] == ""
assert "http" in charvec[n-2]
if charvec[n+1] == "pubmed" and pmid not in good_pmids and pmid not in bad_pmids:
assert(len(pmid)>0)
url = "https://pubmed.ncbi.nlm.nih.gov/" + pmid
try:
if "+" in pmid:
#These make valid URLs, but are invalid URIs: they don't fit the pubmed id pattern.
bad_pmids.add(pmid)
elif urllib.request.urlopen(url).getcode() > 400:
bad_pmids.add(pmid)
else:
good_pmids.add(pmid)
pmids_changed = True
except:
bad_pmids.add(pmid)
if len(charvec) > n+2:
pmid = charvec[n+2]
if charvec[n+1] not in VALID_IDENTIFIERS_NAMESPACES:
# if checkAndAddIdentifiersNamespace(charvec[n+1]):
bad_identifiers_ns.add(charvec[n+1])
assert charvec[n-1] == ""
assert "http" in charvec[n-2]
if charvec[n+1] == "pubmed" and pmid not in good_pmids and pmid not in bad_pmids:
assert(len(pmid)>0)
url = "https://pubmed.ncbi.nlm.nih.gov/" + pmid
try:
if "+" in pmid:
#These make valid URLs, but are invalid URIs: they don't fit the pubmed id pattern.
bad_pmids.add(pmid)
elif urllib.request.urlopen(url).getcode() > 400:
bad_pmids.add(pmid)
else:
good_pmids.add(pmid)
pmids_changed = True
except:
bad_pmids.add(pmid)
f.close()
if pmids_changed:
gp_file = open("good_pmids.p", "wb")
Expand Down
26 changes: 13 additions & 13 deletions manual-fixes/BIOMD0000000001/manifest.xml
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Original file line number Diff line number Diff line change
@@ -1,19 +1,19 @@
<?xml version="1.0" encoding="UTF-8"?>
<omexManifest xmlns="http://identifiers.org/combine.specifications/omex-manifest">
<content location="." format="https://identifiers.org/combine.specifications/omex" master="false"/>
<content location="./BIOMD0000000001-biopax2.owl" format="https://identifiers.org/combine.specifications/biopax.level-2" master="false"/>
<content location="./BIOMD0000000001-biopax3.owl" format="https://identifiers.org/combine.specifications/biopax.level-3" master="false"/>
<content location="./BIOMD0000000001.m" format="https://purl.org/NET/mediatypes/application/x.unknown" master="false"/>
<content location="./BIOMD0000000001.pdf" format="https://purl.org/NET/mediatypes/application/pdf" master="false"/>
<content location="./BIOMD0000000001.png" format="https://purl.org/NET/mediatypes/image/png" master="false"/>
<content location="./BIOMD0000000001.sci" format="https://purl.org/NET/mediatypes/application/x.unknown" master="false"/>
<content location="./BIOMD0000000001.svg" format="https://purl.org/NET/mediatypes/application/xml" master="false"/>
<content location="./BIOMD0000000001.vcml" format="https://purl.org/NET/mediatypes/application/xml" master="false"/>
<content location="./BIOMD0000000001.xpp" format="https://purl.org/NET/mediatypes/application/x.unknown" master="false"/>
<content location="./BIOMD0000000001_manual.png" format="https://purl.org/NET/mediatypes/image/png" master="false"/>
<content location="./BIOMD0000000001_manual.svg" format="https://purl.org/NET/mediatypes/application/xml" master="false"/>
<content location="./BIOMD0000000001_url.xml" format="https://identifiers.org/combine.specifications/sbml.level-2.version-4" master="true"/>
<content location="./BIOMD0000000001_urn.xml" format="https://identifiers.org/combine.specifications/sbml.level-2.version-4" master="false"/>
<content location="./manifest.xml" format="https://identifiers.org/combine.specifications/omex-manifest" master="false"/>
<content location="./metadata.rdf" format="https://identifiers.org/combine.specifications/omex-metadata" master="false"/>
<content location="BIOMD0000000001-biopax2.owl" format="https://identifiers.org/combine.specifications/biopax.level-2" master="false"/>
<content location="BIOMD0000000001-biopax3.owl" format="https://identifiers.org/combine.specifications/biopax.level-3" master="false"/>
<content location="BIOMD0000000001.m" format="https://purl.org/NET/mediatypes/application/x.unknown" master="false"/>
<content location="BIOMD0000000001.pdf" format="https://purl.org/NET/mediatypes/application/pdf" master="false"/>
<content location="BIOMD0000000001.png" format="https://purl.org/NET/mediatypes/image/png" master="false"/>
<content location="BIOMD0000000001.sci" format="https://purl.org/NET/mediatypes/application/x.unknown" master="false"/>
<content location="BIOMD0000000001.svg" format="https://purl.org/NET/mediatypes/application/xml" master="false"/>
<content location="BIOMD0000000001.vcml" format="https://purl.org/NET/mediatypes/application/xml" master="false"/>
<content location="BIOMD0000000001.xpp" format="https://purl.org/NET/mediatypes/application/x.unknown" master="false"/>
<content location="BIOMD0000000001_manual.png" format="https://purl.org/NET/mediatypes/image/png" master="false"/>
<content location="BIOMD0000000001_manual.svg" format="https://purl.org/NET/mediatypes/application/xml" master="false"/>
<content location="BIOMD0000000001_url.xml" format="https://identifiers.org/combine.specifications/sbml.level-2.version-4" master="true"/>
<content location="BIOMD0000000001_urn.xml" format="https://identifiers.org/combine.specifications/sbml.level-2.version-4" master="false"/>
</omexManifest>
26 changes: 13 additions & 13 deletions manual-fixes/BIOMD0000000002/manifest.xml
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Original file line number Diff line number Diff line change
@@ -1,19 +1,19 @@
<?xml version="1.0" encoding="UTF-8"?>
<omexManifest xmlns="http://identifiers.org/combine.specifications/omex-manifest">
<content location="." format="https://identifiers.org/combine.specifications/omex" master="false"/>
<content location="./BIOMD0000000002-biopax2.owl" format="https://identifiers.org/combine.specifications/biopax.level-2" master="false"/>
<content location="./BIOMD0000000002-biopax3.owl" format="https://identifiers.org/combine.specifications/biopax.level-3" master="false"/>
<content location="./BIOMD0000000002.m" format="https://purl.org/NET/mediatypes/application/x.unknown" master="false"/>
<content location="./BIOMD0000000002.pdf" format="https://purl.org/NET/mediatypes/application/pdf" master="false"/>
<content location="./BIOMD0000000002.png" format="https://purl.org/NET/mediatypes/image/png" master="false"/>
<content location="./BIOMD0000000002.sci" format="https://purl.org/NET/mediatypes/application/x.unknown" master="false"/>
<content location="./BIOMD0000000002.svg" format="https://purl.org/NET/mediatypes/application/xml" master="false"/>
<content location="./BIOMD0000000002.vcml" format="https://purl.org/NET/mediatypes/application/xml" master="false"/>
<content location="./BIOMD0000000002.xpp" format="https://purl.org/NET/mediatypes/application/x.unknown" master="false"/>
<content location="./BIOMD0000000002_manual.png" format="https://purl.org/NET/mediatypes/image/png" master="false"/>
<content location="./BIOMD0000000002_manual.svg" format="https://purl.org/NET/mediatypes/application/xml" master="false"/>
<content location="./BIOMD0000000002_url.xml" format="https://identifiers.org/combine.specifications/sbml.level-2.version-4" master="true"/>
<content location="./BIOMD0000000002_urn.xml" format="https://identifiers.org/combine.specifications/sbml.level-2.version-4" master="false"/>
<content location="./manifest.xml" format="https://identifiers.org/combine.specifications/omex-manifest" master="false"/>
<content location="./metadata.rdf" format="https://identifiers.org/combine.specifications/omex-metadata" master="false"/>
<content location="BIOMD0000000002-biopax2.owl" format="https://identifiers.org/combine.specifications/biopax.level-2" master="false"/>
<content location="BIOMD0000000002-biopax3.owl" format="https://identifiers.org/combine.specifications/biopax.level-3" master="false"/>
<content location="BIOMD0000000002.m" format="https://purl.org/NET/mediatypes/application/x.unknown" master="false"/>
<content location="BIOMD0000000002.pdf" format="https://purl.org/NET/mediatypes/application/pdf" master="false"/>
<content location="BIOMD0000000002.png" format="https://purl.org/NET/mediatypes/image/png" master="false"/>
<content location="BIOMD0000000002.sci" format="https://purl.org/NET/mediatypes/application/x.unknown" master="false"/>
<content location="BIOMD0000000002.svg" format="https://purl.org/NET/mediatypes/application/xml" master="false"/>
<content location="BIOMD0000000002.vcml" format="https://purl.org/NET/mediatypes/application/xml" master="false"/>
<content location="BIOMD0000000002.xpp" format="https://purl.org/NET/mediatypes/application/x.unknown" master="false"/>
<content location="BIOMD0000000002_manual.png" format="https://purl.org/NET/mediatypes/image/png" master="false"/>
<content location="BIOMD0000000002_manual.svg" format="https://purl.org/NET/mediatypes/application/xml" master="false"/>
<content location="BIOMD0000000002_url.xml" format="https://identifiers.org/combine.specifications/sbml.level-2.version-4" master="true"/>
<content location="BIOMD0000000002_urn.xml" format="https://identifiers.org/combine.specifications/sbml.level-2.version-4" master="false"/>
</omexManifest>
26 changes: 13 additions & 13 deletions manual-fixes/BIOMD0000000003/manifest.xml
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Original file line number Diff line number Diff line change
@@ -1,19 +1,19 @@
<?xml version="1.0" encoding="UTF-8"?>
<omexManifest xmlns="http://identifiers.org/combine.specifications/omex-manifest">
<content location="." format="https://identifiers.org/combine.specifications/omex" master="false"/>
<content location="./BIOMD0000000003-biopax2.owl" format="https://identifiers.org/combine.specifications/biopax.level-2" master="false"/>
<content location="./BIOMD0000000003-biopax3.owl" format="https://identifiers.org/combine.specifications/biopax.level-3" master="false"/>
<content location="./BIOMD0000000003.m" format="https://purl.org/NET/mediatypes/application/x.unknown" master="false"/>
<content location="./BIOMD0000000003.pdf" format="https://purl.org/NET/mediatypes/application/pdf" master="false"/>
<content location="./BIOMD0000000003.png" format="https://purl.org/NET/mediatypes/image/png" master="false"/>
<content location="./BIOMD0000000003.sci" format="https://purl.org/NET/mediatypes/application/x.unknown" master="false"/>
<content location="./BIOMD0000000003.svg" format="https://purl.org/NET/mediatypes/application/xml" master="false"/>
<content location="./BIOMD0000000003.vcml" format="https://purl.org/NET/mediatypes/application/xml" master="false"/>
<content location="./BIOMD0000000003.xpp" format="https://purl.org/NET/mediatypes/application/x.unknown" master="false"/>
<content location="./BIOMD0000000003_manual.png" format="https://purl.org/NET/mediatypes/image/png" master="false"/>
<content location="./BIOMD0000000003_manual.svg" format="https://purl.org/NET/mediatypes/application/xml" master="false"/>
<content location="./BIOMD0000000003_url.xml" format="https://identifiers.org/combine.specifications/sbml.level-2.version-4" master="true"/>
<content location="./BIOMD0000000003_urn.xml" format="https://identifiers.org/combine.specifications/sbml.level-2.version-4" master="false"/>
<content location="./manifest.xml" format="https://identifiers.org/combine.specifications/omex-manifest" master="false"/>
<content location="./metadata.rdf" format="https://identifiers.org/combine.specifications/omex-metadata" master="false"/>
<content location="BIOMD0000000003-biopax2.owl" format="https://identifiers.org/combine.specifications/biopax.level-2" master="false"/>
<content location="BIOMD0000000003-biopax3.owl" format="https://identifiers.org/combine.specifications/biopax.level-3" master="false"/>
<content location="BIOMD0000000003.m" format="https://purl.org/NET/mediatypes/application/x.unknown" master="false"/>
<content location="BIOMD0000000003.pdf" format="https://purl.org/NET/mediatypes/application/pdf" master="false"/>
<content location="BIOMD0000000003.png" format="https://purl.org/NET/mediatypes/image/png" master="false"/>
<content location="BIOMD0000000003.sci" format="https://purl.org/NET/mediatypes/application/x.unknown" master="false"/>
<content location="BIOMD0000000003.svg" format="https://purl.org/NET/mediatypes/application/xml" master="false"/>
<content location="BIOMD0000000003.vcml" format="https://purl.org/NET/mediatypes/application/xml" master="false"/>
<content location="BIOMD0000000003.xpp" format="https://purl.org/NET/mediatypes/application/x.unknown" master="false"/>
<content location="BIOMD0000000003_manual.png" format="https://purl.org/NET/mediatypes/image/png" master="false"/>
<content location="BIOMD0000000003_manual.svg" format="https://purl.org/NET/mediatypes/application/xml" master="false"/>
<content location="BIOMD0000000003_url.xml" format="https://identifiers.org/combine.specifications/sbml.level-2.version-4" master="true"/>
<content location="BIOMD0000000003_urn.xml" format="https://identifiers.org/combine.specifications/sbml.level-2.version-4" master="false"/>
</omexManifest>
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