Match PubMed MeSH thesaurus with Journal Reference Keywords

I am looking for assistance to match keywords from the PubMed MeSH thesaurus with journal reference keywords to enhance indexing and categorization of articles. This work will be done using automated matching to ensure accuracy and scalability, and needs to be completed for more than 500 journal references. The successful freelancer must have experience with PubMed MeSH thesaurus, journal reference keywords and automated matching, and using Excel and R (statistical) packages. Accurate and timely completion of this project is essential. If you feel that you can fulfill this task, please contact me to discuss further details and project progress.

Background: I have two data sources.

1. A Pubmed download, consisting of 441848 rows (each a journal article reference) and 44 columns (Unique ID, Author, Year, Title, abstract, Keywords etc)

The Pubmed output keywords column contains all words by which each article is marked.

2. The list of Medical Subject Headings (MeSH) is from the United States National Library of Medicine. MeSH is a hierarchical framework.

The MeSH list contains 36056 rows listing the keywords from the 16 areas by which papers are classified/codes (Anatomy [A], Organisms [B], Diseases [C], Chemicals and Drugs [D] etc)

Some headings repeating within one level under different subheadings and/or across more that one level of the hierarchy. But each has a unique identifier (e.g. Anatomic Landmarks;A01.111)

(the tree view can be seen at [login to view URL])

Tasks: I am seeking to – cross reference the MeSH headings with the keywords to obtain a matrix of the keywords in the Pubmed dowload which reflect the 16 areas of the MeSH codes.

One way of approaching this is to:

(a) Rearranging the MeSH headings from long (column) to wide, with each ‘level’ having a unique column e.g. the following would be restructured:

Column 1

Body Regions;A01

Anatomic Landmarks;A01.111

Breast;A01.236

Mammary Glands, Human;A01.236.249

Nipples;A01.236.500

Extremities;A01.378

Amputation Stumps;A01.378.100

To

Column 1 Column 2 Column 3

Body Regions;A01 Anatomic Landmarks;A01.111

Breast;A01.236

Mammary Glands, Human;A01.236.249

Nipples;A01.236.500

Extremities;A01.378

Amputation Stumps;A01.378.100

(b) Parse the words in the Keyword column in the Pubmed download into individual columns

(c) Match the text from MeSH with the PubMed reflecting the structure of the MeSH download.

Note. Keywords in the Pubmed download are not arranged as per the MeSH structure. In addition there are some Keyword in the Pubmed download which are followed by a /’and a qualifier’. In this instances the first word is the word of interest. Attached is the Pubmed file – called PubMed for R, although in Excel formate. And the link the Mesh data is at [login to view URL]

However, I am open to other suggestions. Thank you for your time and consideration.

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