Homework 5 (aka Project)

Due: Monday, December 8, 2024 at 11:59 p.m.
Points: 100

Homework 4 had you produce a list of publication IDs from a keyword search on PubMed. The final project is to produce a list of the publication citations for that keyword.

Begin with your program 4. The program prints out a list of PubMed publication IDs. Use those to get the metadata. The URL for this is:

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&retmode=xml&id=n

where n is a comma-separated list of PubMed publication IDs (or just a single PubMed publication ID). The web page you get back is an XML document giving details of the publications.

Your job is to print a bibliography from this record. Your entry for each journal should look like this:

A. Bester, R. Zelazny, and H. Ellison, "On the Role of Viruses in Future Epidemics," Journal of Future Results 3(4) pp. 29-35 (Mar. 2103). DOI 12.1119/2847595; PUBMED: 23456789.

Then print the abstract, if it is present in the record.

If there is no DOI, omit that part of the entry.

You will need to look at the XML records to get the fields. These are delimited by tags with attributes, each of which may have a value. For example, the element

<ELocationID EIdType="doi" ValidYN="Y">10.1016/j.vaccine.2015.04.071</ELocationID>

has a tag of ELocationID, attributes of EIdType (with value doi) and ValidYN (with a value of Y), and the field contains 10.1016/j.vaccine.2015.04.071, which (as the EIdType value indicates) is a DOI. If its type were “pubmed”, the value would be the PubMed publication ID.

The fields of interest will have these tags:

Journal — this consists of several elements, including JournalIssue, which contains the Volume, Issue, and PubDate (publication date), and Title (article title).
AuthorList — this lists the authors, each author being in a field called Author. Subfields of interest are LastName and Initial (the initial of the first name)

If you want to see what the full structure is, just use the above URL to request a single item. This will also prove helpful in figuring out the attributes and tags you may need.

You can find methods for processing XML in the Python Library Reference at https://docs.python.org/3.14/library/xml.etree.elementtree.html

Matt Bishop
Office: 2209 Watershed Sciences
Phone: +1 (530) 752-8060
Email: mabishop@ucdavis.edu

MHI 289I, Programming in Health Informatics
Version of November 19, 2025 at 9:35PM

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