Re: [CODE4LIB] Public Health Metadata

[Rees, John (NIH/NLM) [E]]

I'm no expert, but +1 for looking at the full UMLS toolkit. There's also a 
semantic UMLS service. I'm sure that Olivier Bodenreider and the UMLS staff 
would be helpful if you made direct inquiries about your use case.


John P. Rees
Archivist and Digital Resources Manager
History of Medicine Division
National Library of Medicine
301-496-8953



-Original Message-
From: Karen Hanson [mailto:karen.han...@ithaka.org] 
Sent: Monday, March 14, 2016 3:38 PM
To: CODE4LIB@LISTSERV.ND.EDU
Subject: Re: [CODE4LIB] Public Health Metadata

MeSH is one of >100 health/biomedical vocabularies listed in UMLS, so I suspect 
there may be other vocabularies in there that are a better fit for public 
health:
https://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/source_faq.html
https://www.nlm.nih.gov/research/umls/sourcereleasedocs/ 

You may need to sign up for a free license in order to browse all vocabularies:
https://www.nlm.nih.gov/databases/umls.html 

Good luck!

Karen Hanson
Research Developer
Portico

-Original Message-
From: Code for Libraries [mailto:CODE4LIB@LISTSERV.ND.EDU] On Behalf Of Jacob 
Ratliff
Sent: Monday, March 14, 2016 2:43 PM
To: CODE4LIB@LISTSERV.ND.EDU
Subject: Re: [CODE4LIB] Public Health Metadata

MeSH is a little helpful, but it is slightly different than the realm of  
public health, which spends a lot of time on the systems surrounding health, as 
well as the health areas themselves. (e.g. Pharmacy supply chain management). 
That's the direction I'm heading though!

Jacob

On Mon, Mar 14, 2016 at 2:35 PM, Carol Bean  wrote:

> MeSH?
>
> Sent from my iPhone
>
> > On Mar 14, 2016, at 1:22 PM, Jacob Ratliff 
> wrote:
> >
> > Hi all,
> >
> > I currently work in an International public health non-profit, and 
> > we
> are setting up enterprise wide document management for dealing with 
> Knowledge Management and Information Management issues. Lots of moving 
> pieces, but I wanted to get some input on metadata specific to the 
> medical/health world. I am looking for some metadata guidance 
> specifically related to the medical/health world. Is anyone using any 
> standard controlled vocabularies? Should I be looking into Linked 
> Data? I'm starting off the research phase for all of the metadata, so 
> links to resources and case studies is greatly helpful!
> >
> > Bonus points to anything that is international in scope, as over 75% 
> > of
> the employees at my company are non-US based (most of them in Africa).
> >
> > Thanks,
> >
> > Jacob Ratliff
> > Information Architect / UX Specialsit Management Sciences for Health 
> > jaratlif...@gmail.com
>

Re: [CODE4LIB] examples of displays for compound objects and metadata

[Rees, John (NIH/NLM) [E]]

See NLM's Fedora/Blacklight implementation for serials: 
http://collections.nlm.nih.gov/catalog/nlm:nlmuid-52420700R-root

Root object metadata is from the MARC record for the whole work; leaf object 
metadata is volume-specific (it's hand-crafted).


John P. Rees
Archivist and Digital Resources Manager
History of Medicine Division
National Library of Medicine
301-496-8953



-Original Message-
From: Laura Buchholz [mailto:laura.buchh...@reed.edu] 
Sent: Wednesday, January 28, 2015 4:44 PM
To: CODE4LIB@LISTSERV.ND.EDU
Subject: [CODE4LIB] examples of displays for compound objects and metadata

We're migrating from CONTENTdm and trying to figure out how to display compound 
objects (or the things formerly known as compound objects) and metadata for the 
end user. Can anyone point me to really good examples of displaying items like 
this, especially where the user can see metadata for parts of the whole? I'm 
looking more for examples of the layout of all the different components on the 
page (or pages) rather than specific image viewers. Our new system is 
homegrown, so we have a lot of flexibility in deciding where things go.

We essentially have:
-the physical item (multiple files per item of images of text, plain text, pdf) 
-metadata about the item -possibly metadata about a part of the item (think 
title/author/subjects for a newspaper article within the whole newspaper 
issue), of which the titles might be used for navigation through the whole item.

I think Hathi Trust has a good example of all these components coming together 
(except viewing non-title metadata for parts), and I'm curious if there are 
others. Or do most places just skip creating/displaying any kind of metadata 
for the parts of the whole?

Thanks for any help!

--
Laura Buchholz
Digital Assets Specialist
Reed College
503-517-7629
laura.buchh...@reed.edu

Re: [CODE4LIB] clarification about file visualization

[Rees, John (NIH/NLM) [E]]

Something like Quick View Plus?

http://www.avantstar.com/metro/home/products/quickviewplusstandardedition

john



-Original Message-
From: Shearer, Timothy J [mailto:tshea...@email.unc.edu] 
Sent: Thursday, August 30, 2012 6:03 PM
To: CODE4LIB@LISTSERV.ND.EDU
Subject: [CODE4LIB] clarification about file visualization

Hi Folks,

My query may have been poorly expressed...

What we have is a webserver with 64,665 files (html, css, js, jpg, you get the 
idea) and lots of directories with subdirectories.

The goal is to be able to conveniently take all that in in a way that makes it 
pretty simple to see/navigate (say for a public services staff member tasked 
with doing a survey of the old content) so that we can get a handle on what's 
there (prior to say, moving from a php+html template approach to a CMS).  It's 
about exploring the website from under the hood.

In my limited imagination it might look like: the document tree represented in 
xml as viewed through a web browser.  Expanding/contracting nodes (and being 
able to recursively explode the view at at any node).
Maybe choose to hide things like image, css, and js files.  Annotation would be 
lovely (say at a subdirectory be able to say: "this one's old and needs to go", 
"this one we keep as is", "this one needs to be reworked entirely").  And in an 
ideal world state could be preserved...if you'd expanded/contracted chunks as 
you were exploring, you could come back later and be where you were in your 
exploration.

tree expresses the file system as (strangely enough) a tree, but the output is 
not interactive and it's huge and unwieldy to deal with.  If you find a 
subdirectory that's full of thousands of files that are irrelevant to the task 
of getting a handle on the overall content, they're on the screen and you page 
and page down and eventually lose track of where they are in the directory 
hierarchy.

I'm more interested in how other shops help users understand a huge old 
webserver's content than focusing on a specific tool such as the one my brain 
imagines.

Thanks for the feedback so far!

Tim

Re: [CODE4LIB] audio transcription software

[Rees, John (NIH/NLM) [E]]

I'm embarking on exactly the same thing, and for films as well. Depending on 
the fidelity of your recording you will get different results using Premier Pro 
in the Adobe Creative Suite 4/5. For modern (2009 recordings) high-fidelity 
audio we only got 80% accuracy.

Dragon still does not work in Keith's scenario. Dragon works ok if you are 
echoing recorded speech, that is if you repeat the recording using your voice. 
The production rate is a little bit better than that of a novice typer, so if 
you have an army of students you might make some headway. I vowed never to 
attempt this again after echoing a 60 minute film.

In the end we are outsourcing the bulk of our transcriptioning.

John


-Original Message-
From: Keith Jenkins [mailto:k...@cornell.edu] 
Sent: Wednesday, May 12, 2010 2:47 PM
To: CODE4LIB@LISTSERV.ND.EDU
Subject: Re: [CODE4LIB] audio transcription software

I tried Dragon Naturally Speaking a couple of years ago.  (After
breaking a wrist in a cycling accident, I figured it might be easier
than one-hand typing, which wasn't true in the case of typing
programming code with lots of curly brackets, indentation, etc.)

Speech-to-text software works best after a training session, in which
the software asks the speaker to read a known text, to calibrate the
software.  I'm not sure how it might work to calibrate for voices on
recordings, but it may be that the software can learn during a
proof-reading process.  Your success for oral history recordings may
depend on the uniqueness of each speakers voice, and the length of
each recording.  (Lots of short recordings of many different speakers
would tend to be harder.)

Keith


On Wed, May 12, 2010 at 2:18 PM, Eric Lease Morgan  wrote:
> Does anybody here use or know of any audio transcription software?
>
> We have a growing number of projects here at Notre Dame that include oral 
> histories. How can these digital files be converted into plain text? Audio 
> transcription software may be the answer?
>
> --
> Eric Lease Morgan
> University of Notre Dame
>

Re: [CODE4LIB] Assigning DOI for local content

[Rees, John (NIH/NLM) [E]]

And DOIs are just a managed implementation of Handles which the IDF created, so 
you could go the Handles route for free. But then you lose the CrossRef 
services, etc. if that is important to you.

John P. Rees, MA, MLIS
Curator, Archives and Modern Manuscripts
History of Medicine Division, MSC 3819
National Library of Medicine
8600 Rockville Pike
Bethesda, MD 20894




-Original Message-
From: Jodi Schneider [mailto:jodi.a.schnei...@gmail.com] 
Sent: Tuesday, November 17, 2009 6:59 PM
To: CODE4LIB@LISTSERV.ND.EDU
Subject: Re: [CODE4LIB] Assigning DOI for local content

The first question is: what are they trying to accomplish by having DOIs?

Do they have a long-term plan for persistence of their content? Financial
plan?

If they're looking for persistent identifiers, I don't understand (a
priori), why DOI is better, as an identifier scheme, than any other
'persistent identifier scheme' (ARK [1], PURL, Handle, etc[2]). (Though I
really like CrossRef and the things they're doing.)

[1] http://www.cdlib.org/inside/diglib/ark/
[2] http://www.persistent-identifier.de/english/204-examples.php

-Jodi

On Tue, Nov 17, 2009 at 11:44 PM, Bucknell, Terry <
t.d.buckn...@liverpool.ac.uk> wrote:

> You should be able to find all the information you need about CrossRef fees
> and rules at:
>
> http://www.crossref.org/02publishers/20pub_fees.html
>
> and
>
> http://www.crossref.org/02publishers/59pub_rules.html
>
> Information about the system of registering and maintaining DOIs is at:
>
> http://www.crossref.org/help/
>
> Note that as well as registering DOIs for the articles in LLT, LLT would be
> obliged to link to the articles cited by LLT articles (for cited articles
> that have DOIs too). Looking at the LLT site, it looks like they would have
> to change their 'abstract' pages to 'abstract plus cited refs', or change
> the way that their PDFs are created so that they include DOI links for cited
> references. (Without this the whole system would fail: publishers would
> expect traffic to come to them, but wouldn't have to send traffic
> elsewhere).
>
> I'd agree that DOIs are in general a Good Thing (and for e-books / e-book
> chapters, and reference work entries as well as e-journal articles). The
> CrossRef fees are deliberately set so as not to exclude single-title
> publishers. Here's an example of a single-title, university-based e-journal
> in the UK that provides DOIs, so it must be a CrossRef member:
> http://www.bioscience.heacademy.ac.uk/journal/.
>
>
> Terry Bucknell
> Electronic Resources Manager
> University of Liverpool
>
>
> -Original Message-
> From: Code for Libraries [mailto:code4...@listserv.nd.edu] On Behalf Of
> Jonathan Rochkind
> Sent: 17 November 2009 23:20
> To: CODE4LIB@LISTSERV.ND.EDU
> Subject: Re: [CODE4LIB] Assigning DOI for local content
>
> So I have no actual experience with this.
>
> But you have to pay for DOI's.  I've never done it, but I don't think
> you neccesarily have to run your own purl server -- CrossRef takes care
> of it.  Of course, if your documents are going to be moving all over the
> place, if you run your own purl server and register your purls with
> CrossRef, then when a document moves, you can update your local purl
> server; otherwise, you can update CrossRef, heh.
>
> It certainly is useful to have DOIs, I agree.  I would suggest they
> should just contact cross-ref and get information on the cost, and what
> their responsibilities are, and then they'll be able to decide.  If the
> 'structure of their content' is journal articles, then, sure DOI is
> pretty handy for people wanting to cite or link to those articles.
>
> Jonathan
>
> Ranti Junus wrote:
> > Hi All,
> >
> > I was asked by somebody from a college @ my institution whether they
> > should go with assigning DOI for their journal articles:
> > http://llt.msu.edu/
> >
> > I can see the advantage of this approach and my first thought is more
> > about whether they have resources in running their purl server, or
> > whether they would need to do it through crossref (or any other
> > agency.) Has anybody had any experience about this?
> >
> > Moreover, are there other factors that one should consider (pros and
> > cons) about this? Or, looking at the structure of their content,
> > whether they ever need DOI? Any ideas and/or suggestions?
> >
> >
> > Any insights about this is much appreciated.
> >
> >
> > thanks,
> > ranti.
> >
> >
>

[CODE4LIB] POSITION ANNOUNCEMENT AT NLM

[Rees, John (NIH/NLM) [E]]

*** 
POSITION ANNOUNCEMENT 
Systems Librarian, History of Medicine Division 
The National Library of Medicine's History of Medicine Division is
seeking a dynamic individual as its Systems Librarian. Duties include
managing hardware, software, and network systems within the Division.

The History of Medicine Division holds a preeminent collection
of the world's published medical literature consisting of about 600,000
books from the 15th to the 20th centuries; about 1,000,000 manuscript
items ranging from the 11th century to the present; and some 60,000 fine
prints, photographs and other graphic materials related to the history
of medicine. HMD also has an active and internationally renowned
exhibitions program. A major function of the Division is to give access
to historical materials and history of medicine exhibitions via its
website: http://www.nlm.nih.gov/hmd  .

Knowledge of the history of medicine is not essential, but a
background in the humanities or the sciences would be helpful. 

Series & Grade: GS-1412-12/13 
Salary range: 66,767.00 - 103,220.00 USD per year 
Applications accepted: Monday, August 27, 2007 to Friday,
September 14, 2007 
This vacancy is open to current permanent Federal employees and
status candidates  . 
To find out more information and to apply, please visit the job
vacancy announcement here:
http://jobsearch.usajobs.opm.gov/getjob.asp?JobID=61619444