I am continuing my work on the Encyclopedia of mtDNA Origins from last time… This is a project that will create mtDNA pages for all named branches of our shared maternal tree. This time I will talk about the ninth requirement, a list of academic journal articles that mention the branch.

Journal Article Requirement

From the first post, we have a user story –What the user wants. As a user with mtDNA results, I would like journal articles that mention the branch.

encyclopedia-of-mtdna-origins-sources-and-resources

This is not nearly as simple as it sounds. First, what official style guide to use? I considered APA vs MLA, and for reasons of personal taste chose APA.

APA Citation Format

To start, I checked the Purdue Owl for specifications on APA journal article citations.

APA style dictates that authors are named last name followed by initials; publication year goes between parentheses, followed by a period. The title of the article is in sentence-case, meaning only the first word and proper nouns in the title are capitalized. The periodical title is run in title case, and is followed by the volume number which, with the title, is also italicized. If a DOI has been assigned to the article that you are using, you should include this after the page numbers for the article. If no DOI has been assigned and you are accessing the periodical online, use the URL of the website from which you are retrieving the periodical.

  • Author, A. A., Author, B. B., & Author, C. C. (Year). Title of article. Title of Periodical, volume number(issue number), pages. http://dx.doi.org/xx.xxx/yyyyy

1) Authors are listed in the same order as in publication: Surname, first initial, and period.

Behar, D.M., Villems, R., Soodyall, H., Blue-Smith, J., Pereira, L., Metspalu, E., Scozzari, R., Makkan, H., Tzur, S., Comas, D. & Bertranpetit, J.

My Back Pages – Bob Dylan

A self-ordained professor’s tongue
Too serious to fool
Spouted out that liberty
Is just equality in school
“Equality,” I spoke the word
As if a wedding vow
Ah, but I was so much older then
I’m younger than that now.

In a soldier’s stance, I aimed my hand
At the mongrel dogs who teach
Fearing not that I’d become my enemy
In the instant that I preach
My existence led by confusion boats
Mutiny from stern to bow
Ah, but I was so much older then
I’m younger than that now.

2) The year of publication comes next. It is in parentheses and followed by a period.

(2008).

3) The title should have the first letter of the first word capitalized. It is followed by a period.

The dawn of human matrilineal diversity.

4) The name of the journal is italicized and followed by a comma.

The American Journal of Human Genetics,

5) The issue and volume are set together with the issue number in parentheses. The volume is italicized. They are followed by a comma.

82(5),

6) The first and last page numbers are separated by a dash and followed by a period.

1130-1140.

I decided to skip the DOI link, because experience tells me that DOI links break. In sum, each citation should look something like this.

  • Behar, D.M., Villems, R., Soodyall, H., Blue-Smith, J., Pereira, L., Metspalu, E., Scozzari, R., Makkan, H., Tzur, S., Comas, D. & Bertranpetit, J. (2008). The dawn of human matrilineal diversity. The American Journal of Human Genetics, 82(5), 1130-1140.

The next question was how to store the article information. Until a few months ago, I used CiteULike as my citation manager.

Journal Article Archive

When I started rebuilding the website this summer, I decided to move my citation collection from CiteULike to the website. I exported a file from CiteULike and discovered that the data stored there is not clean. Despite using their citations collection and update tools, there were many empty fields and inconsistent formating. Thus, the Journal Article Archive is a major work in progress.

It is complete enough for use in the Encyclopedia of mtDNA Origins though. There are eight fields, Author(s), et_al, Journal, Volume & Issue, Page(s), Year, Abstract, and Source Link.

encyclopedia-of-mtdna-origins-journal-articles

Linking Journal Articles to mtDNA Branch Stories

To link between Journal Articles and mtDNA Stories, I added a relationship field for Related mtDNA Stories to the Journal Articles post type.

encyclopedia-of-mtdna-origins-related-mtdna-sources

I made it bidirectional by adding a Related mtDNA Sources field the mtDNA Stories post type.

encyclopedia-of-mtdna-origins-mtdna-related-sources

I then did a little magic with Excel matching between GenBank information on sample sources and a download of the Journal Article Archive. With a bit of SQL, the relationships went into the database.

Adding Citations to Pages

Adding sources to each page required creating a new Get Citation from Journal Articles template and updating the mtDNA Story Template. As in other templates, I used

[before] and [after] tags to start and stop an unordered list. As I said, I did not use DOI links, because they break. Instead, I made the title of each journal article a link to the article’s page in the Journal Article Archive.

Encyclopedia of mtDNA Origins - Get Citation from Journal Articles

Updating the mtDNA Story Template was a couple more lines of code. The code pulls from the Journal Article post type (pod) and sorts results by the et_al field where any related story title matches the current mtDNA Story title. The limit is set to -1 meaning unlimited.

encyclopedia-of-mtdna-origins-mtdna-story-template-related-sources-update

Reviewing Work

With those published, it is time to check an mtDNA Story page.

encyclopedia-of-mtdna-origins-related-sources-example

It looks good. To be continued…