Leverage departmental affiliation string matching for phase two matching

[paulalbert1]

Use "Department of [target author's department(s) as tracked in rc_identity]" to match target co-authors

Sometimes the affiliation of the target co-author in PubMed will explicitly state the department. For example:

• Take Rita Shankovich (ris9004).
• Here - http://www.ncbi.nlm.nih.gov/pubmed/25867473 - is a candidate article in which R. Shankovich is listed as an author
• When you go to the "primary_department" and "primary_affiliation" of that author, it says, "Pathology and Laboratory Medicine" and "Weill Cornell Medical College, Cornell University," respectively.
• Go to rc_identity and look up primary and other departments. They are "Pathology and Laboratory Medicine" and "Medicine"
• Does either "Department of Pathology and Laboratory Medicine" or "Department of Medicine" exist for the target author?
• Not only that, but it also says "Weill Cornell" however... see Helen Fernandes's case below.
• So that match should increase the likelihood we have a match.
• Please be sure to translate "and" into different ways it's represented. "Pathology and Laboratory Medicine" should become:
  • Pathology and Laboratory Medicine
  • Pathology/Laboratory Medicine
  • Pathology & Laboratory Medicine

Other examples:

• Shahin Rafii (srafii) is in the Department of Genetic Medicine, which is what these publications say - 24733255, 24799717
• Fuqiang Geng (fug2001) is in the "Department of Genetic Medicine" and that is listed as this author's affiliation: 24799717 (currently false negative)
• Helen Fernandes (hef9020) is in the "Department of Pathology and Laboratory Medicine" and that is listed as this author's affiliation (currently false negative): 9682005 1382908 11140879 21881595 1467538. Note that these publications were authored while she was at another institution! For example:
  • Department of Pathology, New Jersey Medical School, UMDNJ, Newark 07103, USA. (21881595)
  • Department of Pathology and Lab Medicine, University of Medicine and Dentistry/New Jersey Medical School, Newark, NJ 07103, USA. (11140879)
  • Department of Laboratory Medicine and Pathology, UMDNJ-New Jersey Medical School, Newark 07103. (1382908)

Related to #46

[jl987-Jie]

if (selectingTarget) {
    // Grab columns "primary_department" and "other_departments" from table "rc_identity".
    /*
     * Please be sure to translate "and" into different ways it's represented. "Pathology and Laboratory Medicine" should become:
        1. Pathology and Laboratory Medicine
        2. Pathology/Laboratory Medicine
        3. Pathology & Laboratory Medicine
    */
    /*
    for (ReCiterArticle article : finalCluster.get(id).getArticleCluster()) {
        // compare the above departments information with the article's affiliation information.
        // increase the sim score if departments match.
    }
*/

[jl987-Jie]

    /**
     * Extract Department information from string of the form "Department of *,".
     * 
     * @param department Department string
     * @return Department name.
     */
    private String extractDepartment(String department) {
        final Pattern pattern = Pattern.compile("Department of (.+?),");
        final Matcher matcher = pattern.matcher(department);
        if (matcher.find()) {
            return matcher.group(1);
        } else {
            return "";
        }
    }

    /**
     * Leverage departmental affiliation string matching for phase two matching.
     * 
     * If reCiterAuthor has department information, extract the "department of ***" string and use string comparison
     * to match to target author's primary department and other department fields. If both party's department match,
     * return true, else return false.
     * 
     * (Github issue: https://github.com/wcmc-its/ReCiter/issues/79)
     * @return True if the department of the ReCiterAuthor and TargetAuthor match.
     */
    public boolean departmentMatch(ReCiterAuthor reCiterAuthor, TargetAuthor targetAuthor) {

        if (reCiterAuthor.getAffiliation() != null) {
            String affiliation = reCiterAuthor.getAffiliation().getAffiliationName();
            String extractedDept = extractDepartment(affiliation);
            String targetAuthorDept = targetAuthor.getDepartment();
            String targetAuthorOtherDept = targetAuthor.getOtherDeparment();
            if (extractedDept.equalsIgnoreCase(targetAuthorDept) || extractedDept.equalsIgnoreCase(targetAuthorOtherDept)) {
                return true;
            }
        }
        return false;
    }

[michaelbales1]

Hanumantha has implemented and reports that Jie has integrated his code into his the ReCiterAlgorithmRevisionJul2015 branch.