Difference between revisions of "Bibliographic/OOoBib Functional Requirements/Keywords"

From Apache OpenOffice Wiki
Jump to: navigation, search
(Journals)
(General Medical Journals)
Line 360: Line 360:
 
|  
 
|  
 
| med, all
 
| med, all
 +
| http://www.sciencedirect.com/science/journal/00029343
 
|-
 
|-
 
| Annals of Internal Medicine
 
| Annals of Internal Medicine
Line 366: Line 367:
 
| med, intern
 
| med, intern
 
| http://www.annals.org
 
| http://www.annals.org
 +
|-
 +
| British Medical Journal
 +
| BMJ
 +
| BMJ
 +
| med, all
 +
| http://bmj.bmjjournals.com
 
|-
 
|-
 
| Journal of the American Medical Association
 
| Journal of the American Medical Association
Line 371: Line 378:
 
| JAMA
 
| JAMA
 
| med, all
 
| med, all
 +
| http://jama.ama-assn.org
 
|-
 
|-
 
| Lancet
 
| Lancet

Revision as of 22:20, 19 September 2006

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).

( tell me the title and date and I will inset a link to the message David Wilson )

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 full name of the journal, 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 requires Journal of Antimicrobial Chemotherapy and not J Antimicrob Chemother)
  • others require the abbreviated name (actually most journals fit here)
  • 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


Journal List

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.

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


Infectious Diseases Journals

Full Journal Name Short Journal Name (Abbreviation) Custom Shortcut Journal Category URL
American Journal of Infection Control Am J Infect Control AJIC med, infx http://journals.elsevierhealth.com/periodicals/ymic/issues
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 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
Research in Microbiology Res Microbiol med, infx, microbiol http://www.sciencedirect.com/science/journal/09232508
Review Infectious Diseases Rev Infect Dis med, infx
Scandinavian Journal Infectious Diseases Scand J Infect Dis med, infx
Veterinary Microbiology Vet Microbiol biomed, vet, microbiol
International Journal of Systematic and Evolutionary Microbiology Int J Syst Evol Microbiol IJSEM biomed, med, infx, microbiol http://ijs.sgmjournals.org

General Medical Journals

Full Journal Name Short Journal Name (Abbreviation) Custom Shortcut Journal Category URL
American Journal of Medicine Am J Med med, all http://www.sciencedirect.com/science/journal/00029343
Annals of Internal Medicine Ann Intern Med med, intern http://www.annals.org
British Medical Journal BMJ BMJ med, all http://bmj.bmjjournals.com
Journal of the American Medical Association JAMA JAMA med, all http://jama.ama-assn.org
Lancet Lancet med, all http://www.thelancet.com
New England Journal of Medicine New Engl J Med NEJM med, all http://www.nejm.org

Statistics

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


All Categories

Full Journal Name Short Journal Name (Abbreviation) Custom Shortcut Journal Category URL
Nature Nature all
Science Science all

Cell/ Molecular Biology

Full Journal Name Short Journal Name (Abbreviation) Custom Shortcut Journal Category URL
Journal of Biological Chemistry J Biol Chem JBC biomed, cell biol, chem
Proceedings of the National Academy of Sciences of the USA Proc Natl Acad Sci USA PNAS biomed, cell biol, all

Oxford Journals

incomplete - Still need to do a lot of work!!! When I'll finish, I will move these entries in their respective category.

Age and Ageing Age Ageing med, geront http://ageing.oxfordjournals.org/
Alcohol and Alcoholism Alcohol Alcohol med, behav http://alcalc.oxfordjournals.org/
American Journal of Epidemiology Am J Epidemiol med, epidem http://aje.oxfordjournals.org/
Annals of Occupational Hygiene Ann Occup Hyg med, epidem, hygiene http://annhyg.oxfordjournals.org/
Annals of Oncology Ann Oncol med, oncol http://annonc.oxfordjournals.org/
BJA: British Journal of Anaesthesia Br J Anaesth BJA med, ICU http://bja.oxfordjournals.org/
Brain Brain med, neuro http://brain.oxfordjournals.org/
Brief Treatment and Crisis Intervention Brief Treat Crisis Interven med, behav http://brief-treatment.oxfordjournals.org/
British Medical Bulletin Br Med Bull med, all http://bmb.oxfordjournals.org/
Continuing Education in Anaesthesia, Critical Care & Pain Contin Educ Anaesth Crit Care Pain med, ICU http://ceaccp.oxfordjournals.org/
Europace Europace med, cardio http://europace.oxfordjournals.org/
European Heart Journal Eur Heart J med, cardio http://eurheartj.oxfordjournals.org/
The European Journal of Orthodontics Eur J Orthod med, dentist http://ejo.oxfordjournals.org/
The European Journal of Public Health Eur J Public Health med, epidem http://eurpub.oxfordjournals.org/
Evidence-based Complementary and Alternative Medicine Evid Based Complement Alternat Med eCAM med, alt http://ecam.oxfordjournals.org/
Family Practice Fam Pract med http://fampra.oxfordjournals.org/


GAWK HELPER SCRIPT

This script will format the table text for use on this wiki page.


Requirements:

  • awk/gawk:
    • if you are on a UNIX machine, almost surely you will have it installed on your computer
    • if you're on a WINDOWS machine, almost surely you won't have it; you can get a gawk for free from www.sourceforge.net project gnuwin32

Use:

  • Save your Journal Table as a plain text file, with the cells separated by tab and the rows as separate lines
  • Svae the following script as a file, e.g. this-script-file.awk
  • run the gawk script, e.g. gawk -f "this-script-file.awk" your-plain-text-file.txt
  • the script will create a new text file, Journals-OOo.txt, that will contain the formatted text, suitable to paste into this wiki page


GAWK SCRIPT

BEGIN {
	val = ""
	intro = "{| cellspacing=\"0\" cellpading=\"5\" border=\"1\""
	print intro >> "Journals-OOo.txt"
} # END BEGIN


# START ACTUAL PROGRAM <------------------------------------>

# DELETE SPACES

/  /	{ gsub(/  +/, " ")  } # DELETE MULTIPLE SPACES
/^ /	{ gsub(/^ / , "" )  } # REMOVE TRAILING SPACES
/ $/	{ gsub(/ $/ , "" )  } # REMOVE TRAILING SPACES



{if(length($0) == 0) {next} } # SKIP EMPTY LINES


/\t/ {gsub(/\t/,"\n| ")}

{
	print "|-\n| " $0 >> "Journals-OOo.txt"
}

END {
	print "|}" >> "Journals-OOo.txt"
}
Personal tools