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TOOLS

Extract MeSH Descriptors process

The PubMed Related Citations algorithm returns a scored and ranked list of the 20 most relevant citations in HTML format similar to the following sample:

<HTML>
<HEAD>
<TITLE>neighbouring</TITLE>
</HEAD>
<BODY bgcolor="ffffff">
<br><pre><b>The neighbours are:</b></pre><hr>
(1)&nbsp;&nbsp;
    97.027&nbsp;&nbsp;Rosenbaum JL, Almli CR, Yundt KD, Altman DI, Powers WJ<br>
    <A href="http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=9339686">9339686</A>
    &nbsp;&nbsp;Higher neonatal cerebral blood flow correlates with worse childhood neurologic outcome.<hr>
(2)&nbsp;&nbsp;
    33.9859&nbsp;&nbsp;Altman DI, Powers WJ, Perlman JM, Herscovitch P, Volpe SL, Volpe JJ<br>
    <A href="http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=3263081">3263081</A>
    &nbsp;&nbsp;Cerebral blood flow requirement for brain viability in newborn infants is lower than in adults.<hr>

...

(20)&nbsp;&nbsp;
    24.6715&nbsp;&nbsp;Bednarczyk EM, Rutherford WF, Leisure GP, Munger MA, Panacek EA, Miraldi FD, Green JA<br>
    <A href="http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=2343589">2343589</A>


Once we have this data, we do the following for each of the 20 relevant citations returned:

  1. Parse the output to find the score and reference UID for each of the 20 citations.

  2. Call the NCBI Text Tool Server for each of the 20 relevant citation UIDs. This retrieves the citation from PubMed in MEDLINE format which allows us to then parse out the MeSH Headings (lines with "MH -"). The output looks similar to the following sample:

	UI  - 97479605
	PMID- 9339686
	DA  - 19971114
	DCOM- 19971114
	LR  - 20001218
	IS  - 0028-3878
	VI  - 49
	IP  - 4
	DP  - 1997 Oct
	TI  - Higher neonatal cerebral blood flow correlates with worse childhood
	      neurologic outcome.
	PG  - 1035-41
	AB  - Cerebral blood flow (CBF) in newborn infants is often below levels
	      necessary to sustain brain viability in adults. Controversy exists
	      regarding the effects of such low CBF on subsequent neurologic function.
	      We determined the current childhood neurologic status and IQ in 26
	      subjects who had measurements of CBF performed with PET in the neonatal
	      period between 1983 and 1989 as part of a study of hypoxic-ischemic
	      encephalopathy. Follow-up information at ages 4 to 12 years was obtained
	      on all 26 subjects. Ten subjects had died. All 16 survivors underwent
	      clinical neurologic evaluation, and 14 also underwent intelligence
	      testing. Eight had abnormal clinical neurologic evaluations; eight were
	      normal. The mean neonatal CBF in those with abnormal childhood neurologic
	      outcome was significantly higher than in those with normal childhood
	      neurologic outcome (35.64 +/- 11.80 versus 18.26 +/- 8.62 mL 100 g(-1)
	      min(-1), t = 3.36, p = 0.005). A significant negative correlation between
	      neonatal CBF and childhood IQ was demonstrated (Spearman rank correlation
	      r = -0.675, p = 0.008). Higher CBF was associated with lower IQ. The
	      higher CBF in subjects with worse neurologic and intellectual outcome may
	      reflect greater loss of cerebrovascular autoregulation or other vascular
	      regulatory mechanisms due to more severe brain damage.
	AD  - Department of Pediatrics, Washington University School of Medicine, St.
	      Louis Children's Hospital, MO 63110, USA.
	AU  - Rosenbaum JL
	AU  - Almli CR
	AU  - Yundt KD
	AU  - Altman DI
	AU  - Powers WJ
	LA  - eng
	ID  - NS06833/NS/NINDS
	ID  - NS32568/NS/NINDS
	PT  - Journal Article
	CY  - UNITED STATES
	TA  - Neurology
	JC  - NZ0
	JID - 0401060
	SB  - AIM
	SB  - IM
	MH  - Cerebrovascular Circulation/*physiology
	MH  - *Child Development
	MH  - Follow-Up Studies
	MH  - Human
	MH  - Infant, Newborn
	MH  - Intelligence
	MH  - *Nervous System Physiology
	MH  - Neurologic Examination
	MH  - Support, Non-U.S. Gov't
	MH  - Support, U.S. Gov't, P.H.S.
	MH  - Tomography, Emission-Computed
	EDAT- 1997/10/27 20:29
	MHDA- 1997/10/27 20:29
	PST - ppublish
	SO  - Neurology 1997 Oct;49(4):1035-41.

Once we have the citation from PubMed, we need to do the following:
  1. Pull the MeSH Heading ("MH - ") lines from the citation.

  2. Track whether the MeSH Heading is an IM term or not.

  3. Combine the MH with the appropriate UI and original score from the relevant citation we are working on.

  4. The final output of this process is a scored and ranked list of all MeSH Headings from the 20 relevant citations with a line of "***" separating each of the relevant citation's MeSH Headings. The output would look similar to the following:

        97479605|IM|Brain|33.9859 
        97479605|IM|Brain Diseases|33.9859 
        97479605|IM|Cerebrovascular Circulation|33.9859 
        97479605|NIM|Gestational Age|33.9859 
        97479605|NIM|Infant, Premature|33.9859 
        97479605|IM|Tomography, Emission-Computed|33.9859 
        *** 
        97479605|NIM|Asphyxia Neonatorum|29.0115 
97479605|IM|Brain|29.0115
97479605|IM|Brain Ischemia|29.0115
97479605|IM|Cerebrovascular Circulation|29.0115
97479605|IM|Hypoxia, Brain|29.0115
97479605|IM|Intracranial Pressure|29.0115
97479605|IM|Oxygen|29.0115
97479605|NIM|Prognosis|29.0115 *** ... ***
97479605|IM|Cerebrovascular Circulation|24.6715
97479605|NIM|Hypercapnia|24.6715
97479605|IM|Hyperventilation|24.6715
97479605|NIM|Oxygen Radioisotopes|24.6715
97479605|NIM|Tomography, Emission-Computed|24.6715 ***