Harvard:Biophysics 101/2007/Notebook:Resmi Charalel/2007-5-1
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Update
- I have been out of town since last Thursday's class for a revisit weekend and did not have email/computer access there. So, unfortunately, I did not get as much to work on this program as much as I had hoped. But, I definitely plan to continue working on the program and contributing to the project further over the next couple weeks and hope to be able to stay involved this summer.
- So, I have written all of the code to appropriately:
- 1) Parse through OMIM records and obtain all associated PMIDs
- 2) Search all obtained PMIDs in PubMed to return XML output
- 3) Parse the XML output of PubMed for each entry to return the MeshTerms that are labelled as major
- 4) Take the entry title of OMIM and search this in PubMed
- 5) Return the references of the top five PubMed review articles associated with this condition/name as further reading on the general allelic variant
- However, there is still one error in the program, which is difficult to understand and through which I am still working. Here it is:
Traceback (most recent call last): File "/Users/resmicharalel/Documents/biophysics101/pubmed.py", line 93, in <module> m = extract_meshterms(cur_record) File "/Users/resmicharalel/Documents/biophysics101/pubmed.py", line 60, in extract_meshterms dom = parseString(str) File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/xml/dom/minidom.py", line 1923, in parseString return expatbuilder.parseString(string) File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/xml/dom/expatbuilder.py", line 940, in parseString return builder.parseString(string) File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/xml/dom/expatbuilder.py", line 223, in parseString parser.Parse(string, True) TypeError: Parse() argument 1 must be string or read-only buffer, not instance"
- The following is the code thus far:
from Bio.EUtils import DBIdsClient import xml.dom.minidom from xml.dom.minidom import parse, parseString # C-style struct to pass parameters class AllelicVariant: pass class PubmedID: pass class MeshTerms: pass # queries the database and returns all info in an XML format def omim_snp_search(dnsnp_id): client = DBIdsClient.DBIdsClient() query = client.search(dnsnp_id, "omim") records = [i.efetch(rettype="xml") for i in query] return records # basic text extraction from XML; based on http://docs.python.org/lib/dom-example.html def get_text(node_list): rc = "" for node in node_list: if node.nodeType == node.TEXT_NODE: rc = rc + node.data return rc # extracts allelic variant data, as the name implies, using the struct above def extract_allelic_variant_data(str): dom = parseString(str) variants = dom.getElementsByTagName("Mim-allelic-variant") # print "variant:", variants if len(variants) == 0: return parsed = [] for v in variants: a = AllelicVariant() # create empty instance of struct # now populate the struct a.name = get_text(v.getElementsByTagName("Mim-allelic-variant_name")[0].childNodes) a.mutation = get_text(v.getElementsByTagName("Mim-allelic-variant_mutation")[0].getElementsByTagName("Mim-text_text")[0].childNodes) a.description = get_text(v.getElementsByTagName("Mim-allelic-variant_description")[0].getElementsByTagName("Mim-text_text")[0].childNodes) parsed.append(a) return parsed def extract_allelic_variant_pmid(str): dom = parseString(str) pmids = dom.getElementsByTagName("Mim-reference") if len(pmids) == 0: return ids = [] for p in pmids: i = PubmedID() i.pmid = get_text(p.getElementsByTagName("Mim-reference_pubmedUID")[0].childNodes) ids.append(i.pmid) return ids def extract_meshterms(str): dom = parseString(str) meshheadings = dom.getElementsByTagName("MeshHeading") if len(meshterms) == 0: return meshterms = [] for h in meshheadings: m = MeshTerms() m = get_text(h.getElementsByTagName("DescriptorName MajorTopicYN")[0].childNodes) if m == "Y": mesh = get_text(h.getElementsByTagName("DescriptorName")[0].childNodes) meshterms.append(mesh) return meshterms from Bio import PubMed from Bio import Medline import string rec_parser = Medline.RecordParser() medline_dict = PubMed.Dictionary(parser = rec_parser) for i in omim_snp_search("rs11200638"): result = i.read() if result: v = extract_allelic_variant_data(result) p = extract_allelic_variant_pmid(result) if v != None: for a in v: print a.name print a.mutation print a.description if p != None: for s in p: cur_record = medline_dict[s] m = extract_meshterms(cur_record) if m != None: for mh in m: print mh #if p != None: # for i in p: #print i.pmid disease = a.name search_term = "Review[ptyp] "+disease #print search_term review_ids = PubMed.search_for(search_term) ##rec_parser = Medline.RecordParser() ##medline_dict = PubMed.Dictionary(parser = rec_parser) ## count = 1 for did in review_ids[0:5]: cur_record = medline_dict[did] print '\n', count, ') ', string.rstrip(cur_record.title), cur_record.authors, string.strip(cur_record.source) count=count+1 ##for i in omim_snp_search("rs11200638"): ## result = i.read() ## if result: ## p = extract_allelic_variant_pmid(result) ## if p != None: ## key_source = PubMed.search_for(p[0]) ## key_rec = medline_dict[0] ## print key_rec ## ## keywords = get_text(key_rec.getElementsByTagName("MeshHeading")[0].childNodes) ## print keywords
- Also, I am working on better annotating this code so that it is easier to read through and understand for anyone interested in working with it.