Bibliographic/OOoBib Functional Requirements/Keywords

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This document has been placed on the wiki so that members of the OpenOffice community can assist in developing the design and documentation for the enhanced bibliographic facility.

Back to OOoBib Functional Requirements

Keywords

One way to better sort articles is based on Keywords (see my post on keywords).

However, there is another way I will shortly describe here.

There are a number of categories a research paper can belong to:

  • Basic Research
  • Theoretical Research (especially in Math/Physics)
  • Modeling
  • Trials:
    • randomized controlled trial
    • Meta-analysis
    • other trial
  • Review
  • Guideline
  • Correspondence
  • Editorial
  • Epidemiologic Study
  • Case Report
  • Images in clinical medicine (some Journals have such a feature/ could be a subgroup of Case Report)
  • Questions/ Question-Answers

If there are other relevant categories, feel free to implement them as well.

This is especially useful when searching for all trials on a given matter (e.g. for writing a meta-analysis or writing a review or a guideline), or for a specific case report.

I do have some >2500 of articles saved on my computer and searching for the correct file is a nightmare. It may seem that 2500 articles is a huge number, however in infections diseases this is only a minimum to start with.

It is useful to have a field storing this information. Although custom fields exist, this is a feature that should be standard. It allows searching (and grouping) articles on a more powerful basis.

Submitted as issue number 66353 by discoleo at Openoffice.org.

Implementation ideas

How should this be implemented ? Most bib and document systems I have seem to think that adding a field for keywords is enough and let the user the invent their own categories. I have been involved in IT development and document management systems and have had enough lectures from librarians (ie professional indexers) to know that this just leads to a big unmanageable mess, which librarians are often called in to try to fix.

Also a good keyword system has a good set of aliases defined. One insurance company was providing different compensation for fractured limbs than for broken limbs, because their compensation history search system did not have these aliases defined. The cases and the compensation history diverged as each of the staff used their preferred term.

So --- Should we build pre-defined document category sets that a user could select one for each document collection. i.e. Medical Research, Physical Sciences, Social Sciences etc ? David Wilson

Discussion

After a thorough thought, I believe more and more, that a standardization is both highly useful and needed.

I wish to discuss 2 points: 

* how to standardize
* how to implement the standardization

Why Standardise

As more and more research data becomes available, it becomes increasingly difficult to efficiently use this data. The problem stems from the simple fact, that you do NOT get what you want. Most of the published data will end somewhere in the nirvana of computer storage, without beeing ever read by those who would benefit most of it. This problem is likely to deepen in the near future, as more and more journals appear and huge ammounts of data are published.

Even now, I do have serious problems when searching for something. There is so much available literature, that I get easily overwhelmed, although, most of that is not what I need. Refining a search is becoming increasingly difficult, and the time spent on searching can exceed the time needed to read the actuall article.


How to standardise

This is a huge task and, because there is no standardization to date, I belive there is a reason. Therefore, before starting from scratch, it would be wise to search for work already done:

  • search for standards
  • contact librarians, other groups
  • contact others who might be interested or have done work in this field (e.g. Pubmed; I have contacted the Pubmed team and hope for an answer)

Some journals already sort their articles based on some specific features (e.g. Circulation - the journal of the American Heart Association; Chest, and others). Therefore, it could be somewhat more easy to implement some of the standardisation, because professional societies do use them. However, other fields are covered less well and could cause some pain.

Probably it is the best thing to ask the professional societies to create such a framework.

How to implement this

In order to be used in practice, the end-user needs to be served everything already done. Therefore, the program MUST already suggest some appropriate categories. This could be more easily accomplished for major article category, but for more detailed keywords it will become increasingly difficult. (YES, I believe that even the keywords should be standardized, ... maybe sometime in the future.)

Specific procedure:

  • scan journal title: jounals publish in most instances only articles from very specific fields (except maybe Nature and Science)
  • scan title and abstract for some standard words
  • depending on the words found, propose to the user an article category/ subcategory: e.g. medicine/ surgery/ randomized controlled trial

I will continue in the next section with a more thorough discussion of this implementation.

Requirements

Keywords

  • alias: this is a synonyms for a specific word, i.e., the 2 words are equivalent
  • 'hierarchical node': the presence of one term implies automatically another term, although the 2 are not aliases/synonyms, e.g. endocarditis implies infection, bacteremia, heart valves and medicine, too. Another non-medical example: whale implies both mammal and ocean (or water), but mammal does not imply whale.

Article Categories

The article category should contain both the field of work (e.g. medicine) and the type of article (e.g. review). Therefore we should have:

  • category: see Journal Classification below
  • article type: see at the top of this page


Journal Classification

This describes what is needed to implement a standardized journal classification.

We need to define/create lists with:

  • basic categories: this needs to be defined at the top of the hierarchy; every article belongs to one (or more) of these basic categories
  • list of journals: needed for the next point;
  • basic category for journals: we will need to apply one or more categories to every journal.

Basic Field / Top Categories

Question: Do we need subcategories OR, more specifically, how do we define subcategories?

Some journals sort the articles based on some standardised subcategories (this would be usually the 3rd-4th item in the hierarchy):


These lists are incomplete. Please fill in whenever you find additional information.

Various editors sort their publications based on comprehensive speciality lists, e.g. http://www.us.elsevierhealth.com/Medicine

Top Categories

  • mathematics
  • physics
    • quantum mechanics (these would be subcategories, ... or still main categories)
    • astrophysics
    • others
  • biology: part of biomedical sciences?
  • biomedical sciences
    • non-surgical/internal medicine
      • cardiology
      • endocrinology
        • diabetology
      • gastroenterology
        • hepatology
      • haematology/ hematology
      • infectious diseases: should be separate entity?
      • pulmology/ respiratory medicine
      • nephrology
      • neurology
      • geriatric medicine: one node higher?
      • immunology/ rheumatology: should be separate?
      • many subspecialities
    • dermatology
    • intensive care / critical care
    • cognitive sciences/ psichiatry
    • paediatrics/ pediatrics
    • radiology
    • surgery
      • abdominal surgery
      • cardio-vascular surgery/ cardiothoracic surgery
      • emergency medicine
      • obstetrics and gynecology
      • neurosurgery
      • ophthalmology
      • orthopedics
      • otolaryngolgy/ ent surgery
      • plastic surgery
      • urology
      • many subspecialities
    • dentistry
    • nursing

Should these be higher categories

    • infectious diseases
      • microbiology (could be one hierarchical node higher)
      • virology
      • parasitology
      • tropical medicine
      • epidemiology
    • microbiology (could be subspeciality of infectious diseases)

Feel free to expand this list!!!

Journals

This list will include the journals full name, the abbreviated name and the journal category.

Please note, that this list is important NOT only for this feature:

  • some journals require the FULL journal name in the bibliography (e.g. JAC would require Journal of Antimicrobial Chemotherapy)
  • others require the abbreviations (actually most journals)
  • some journals have very short aliases (like JAC, CID, NEJM), which I would like to use when entering by hand a bibliographic entry, BUT this is not the official abbreviation and should therefore automatically be converted to the official abbreviation


I DO NOT KNOW HOW TO CREATE A TABLE!!! PLEASE HELP!!!

Journal List

The Format should be:

(the individual columns are written as separate rows, however the webbrowser will display everything on one row)


Full Journal Name - Short Journal Name (Abbreviation) - Custom Shortcut - Journal Category -

I have this list as an OOo Writer document, too. (contains tables) I will expand it whenever I have time.

One useful addition to this list would be the journal's url.


Infectious Diseases Journals

American Journal of Infection Control Am J Infect Control AJIC med, infx

Antimicrobial Agents and Chemotherapy Antimicrob Agents Chemother AAC med, infx, abx

Chemotherapy Chemotherapy -- med

Clinical Infectious Diseases Clin Infect Dis CID med, infx

Clinical Microbiology Reviews Clin Microbiol Rev CMR med, infx

Emerging Infectious Diseases Emerg Infect Dis

med, infx

European Journal of Clinical Microbiology Eur J Clin Microbiol -- med, infx

European Journal of Clinical Microbiology and Infectious Diseases Eur J Clin Microbiol Infect Dis -- med, infx

Infection Infection -- med, infx

Infection Control Hospital Epidemiology Infect Control Hospital Epidemiol -- med, infx

Infectious Disease Clinics of North America Infect Dis Clin N Am -- med, infx

International Journal of Antimicrobial Agents Int J Antimicrob Agents -- med, infx, abx

Journal of Antimicrobial Chemotherapy J Antimicrob Chemother JAC med, infx, abx

Journal of Bacteriology J Bacteriol -- med, infx

Journal of Biological Chemistry J Biol Chem JBC biomed, cell biol, chem

Journal of Clinical Microbiology J Clin Microbiol JCM med, infx

Journal of Hospital Infection J Hosp Infect -- med, infx

Journal of Infectious Diseases J Infect Dis JID med, infx

Journal of Medical Microbiology J Med Microbiol JMM med, infx, microbiol

Microbes and Infection Microbes Infect -- med, infx

Microbiological Reviews Microbiol Rev -- med, infx, microbiol

Proceedings of the National Academy of Sciences of the USA Proc Natl Acad Sci USA PNAS biomed, cell biol, all

Research in Microbiology ??? -- med, infx, microbiol

Review Infectious Diseases Rev Infect Dis -- med, infx

Scandinavian Journal Infectious Diseases Scand J Infect Dis -- med, infx

Veterinary Microbiology Vet Microbiol -- biomed


General Medical Journals

New England Journal of Medicine New Engl J Med NEJM med, all

Lancet Lancet -- med, all

Journal of the American Medical Association JAMA JAMA med, all

American Journal of Medicine Am J Med -- med, all


Statistics

Journal of Statistical Software, http://www.stat.ucla.edu/journals/jss/


All Categories

Nature Nature -- all

Science Science -- all

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