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create_metadata_rdf.py
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create_metadata_rdf.py
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# -*- coding: utf-8 -*-
"""
Created on Tue Mar 21 12:33:50 2023
@author: Lucian
"""
import os
import libsbml
from biosimulators_utils.ref.utils import get_reference
from biosimulators_utils.config import get_config
from biosimulators_utils.ref.utils import get_pubmed_central_open_access_graphics
from biosimulators_utils.omex_meta.io import BiosimulationsOmexMetaWriter
from biosimulators_utils.omex_meta.data_model import OmexMetadataOutputFormat
import Bio.Entrez
Bio.Entrez.email = '[email protected]'
import operator, glob
import requests
import time
class NonStandardRef():
""" Journal article not from pubmed or doi
"""
citation: str = None
uri: str = None
title: str = None
authors: str = None
date: str = None
pubmed_central_id = None
def __init__(self, citation, uri, title):
self.citation = citation
self.uri = uri
self.title = title
def get_citation(self):
return self.citation
def get_uri(self):
return self.uri
no_pubmed_or_doi = {
"BIOMD0000000358" : NonStandardRef('Stortelder, Walter JH, Pieter Wilhelm Hemker, and Hendrik Coenraad Hemker. "Mathematical modelling in blood coagulation: simulation and parameter estimation." Modelling, Analysis and Simulation [MAS] R 9720 (1997).', "http://www.narcis.nl/publication/RecordID/oai:cwi.nl:4725", "Mathematical modelling in blood coagulation : simulation and parameter estimation"),
"BIOMD0000000454" : 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."),
"BIOMD0000000455" : 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."),
"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()
if master:
note = None
notes = model.getNotes()
if notes:
note = notes.getChild(0).toXMLString()
metadata['description'] = note
metadata['title'] = model.getName()
annotations = model.getAnnotation()
cvterms = libsbml.CVTermList()
libsbml.RDFAnnotationParser.parseRDFAnnotation(annotations, cvterms)
for cv in range(cvterms.getSize()):
cvterm = cvterms.get(cv)
for r in range(cvterm.getNumResources()):
rURI = cvterm.getResourceURI(r)
if "pubmed/" in rURI:
pmid = rURI.split("/")[-1]
pubmedIDs.add(pmid)
if "identifiers.org/doi/" in rURI:
uripos = rURI.find("org/doi/")
doiIDs.add(rURI[uripos+8:])
def addCitationsToMetadata(pubmedIDs, doiIDs, masterID, metadata, id, temp_entry_dir):
citations = []
mastercitation = None
if "pubmed" in masterID:
mastercitation = get_reference(pubmed_id=masterID.split("/")[-1])
time.sleep(2.0)
elif "doi" in masterID:
doivec = masterID.split("doi/")
mastercitation = get_reference(doi=doivec[-1])
time.sleep(2.0)
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)
citations.append(citation)
time.sleep(2.0)
for doiID in doiIDs:
citation = get_reference(doi=doiID)
citations.append(citation)
time.sleep(2.0)
if len(citations)==0:
citations.append(mastercitation)
citations = sorted(citations, key=lambda x : x.get_citation())
for citation in citations:
cite = {
"uri": citation.get_uri(),
"label": citation.get_citation(),
}
metadata['citations'].append(cite)
# if citation.pubmed_central_id:
# thumbnails = get_pubmed_central_open_access_graphics(
# citation.pubmed_central_id,
# temp_entry_dir,
# )
# fileList = glob.glob(temp_entry_dir + '/*.tar.gz')
# # Iterate over the list of filepaths & remove each file.
# for filePath in fileList:
# os.remove(filePath)
# metadata['thumbnails'] = [os.path.relpath(thumbnail.filename, temp_entry_dir).replace("\\", "/") for thumbnail in thumbnails]
if mastercitation.title:
metadata['title'] = mastercitation.title
if mastercitation.authors:
metadata['authors'] = mastercitation.authors
if mastercitation.date:
metadata['date'] = mastercitation.date
def addThumbnailToMetadata(metadata, temp_entry_dir):
for root, dirs, files in os.walk(temp_entry_dir):
for file in files:
if file[-4:] == ".png":
if 'thumbnails' not in metadata:
metadata['thumbnails'] = []
metadata['thumbnails'].append(file)
def getMasterRefFromBiomodels(id):
req = requests.post("https://www.ebi.ac.uk/biomodels/" + id + "?format=json")
req.raise_for_status()
res = req.json()
return res["publication"]["link"]
def run(id, sbml_filenames, temp_entry_dir, sbml_master):
metadata = {
"combine_archive_uri": 'http://omex-library.org/' + id + '.omex',
"uri": '.',
'citations': [],
'keywords': [
'Biomodels',
],
# 'contributors': ["The Biomodels Curation Team", "The Center for Reproducible Biomedical Modeling"]
}
pubmedIDs = set()
doiIDs = set()
masterID = getMasterRefFromBiomodels(id)
if "http://identifiers.org/pubmed/24285357" == masterID:
masterID = "http://identifiers.org/pubmed/24757149"
if "http://identifiers.org/pubmed/25771250" == masterID:
masterID = "http://identifiers.org/pubmed/26148348"
for filename in sbml_filenames:
master = False
if sbml_master in filename:
master = True
parseDocAndAddToMetadata(filename, metadata, master, pubmedIDs, doiIDs)
addCitationsToMetadata(pubmedIDs, doiIDs, masterID, metadata, id, temp_entry_dir)
addThumbnailToMetadata(metadata, temp_entry_dir)
metadata_filename = os.path.join(temp_entry_dir, 'metadata.rdf')
config = get_config()
# config.OMEX_METADATA_OUTPUT_FORMAT = OmexMetadataOutputFormat.turtle
BiosimulationsOmexMetaWriter().run([metadata], metadata_filename, config=config)