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Topic: PMIDs

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	[No title]
		The syntax for the pmid specification has been chosen to help manage the alloca tion of PMIDs across disjoint and autonomous domains of administration and implementation.
		This hierarchic numbering scheme is intended to mirror the implementation hierarchy of performance metric domain, metrics cluster (data structure or operational similarity) and individual metric.
		These macros for the initial components of the pmid are likely to be defined either in a standard include file, e.g.
	www.ibiblio.org /gferg/ldp/man/man4/pmns.4.html (910 words)

	MyMED: A database system for biomedical research on MEDLINE data
		The PMID is an integer of up to eight digits in length that is present in all citations and cannot have an empty value.
		This table is necessary because the PMID value is not known until a second pass through the table with an SQL update statement that extracts it and updates the corresponding rows.
		After all citations are inserted into the citation table, the PMIDs are extracted and inserted for each row because it is not possible to extract the CLOB and an element from within the CLOB at the same time.
	www.research.ibm.com /journal/sj/434/lewis.html (5364 words)

	The Ultimate PMID - American History Information Guide and Reference
		PMID is an acronym for PubMed Identifier or more specifically PubMed Unique Identifier which is a unique number assigned to each PubMed citation of life sciences and biomedical scientific journal articles.
		By using the PMID as a search argument (with of without the [uid] field tag), the relevant abstract with be displayed by PubMed.
		Multiple PMIDs in one search will yield all abstracts (it is interpreted as an OR operation).
	www.historymania.com /american_history/PMID (210 words)

	[No title]
		Not all PMIDs need be represented in the PMNS of every application.
		Internally (below the PMAPI) the implementation of the Performance Metrics Collection System (PMCS) uses only the PMIDs, and a PMNS provides an external mapping from a hierarchic taxonomy of names to PMIDs that is convenient in the context of a particular system or particular use of the PMAPI.
		This means applications need to be aware that metric instantiation is guaranteed to be valid at the time of collection only.
	www.ibiblio.org /gferg/ldp/man/man3/PMAPI.3.html (1754 words)

	Update of TREC 2004 Genomics Track Data (Site not responding. Last check: 2007-11-06)
		Data from the TREC 2004 Genomics Track were updated in early 2005 due to concerns that the MGI GO annotation files were substantially updated enough from the original "snapshot" of data in the spring of 2004 to change the results of experiments.
		The status of PMIDs could change because MGI decided to annotate an article it had not previously assessed for triage or because it had decided to not annotate an article after it was initially triaged for annotation.
		We updated the triage subtask files by adding the PMIDs newly designated for GO annotation or newly annotated and subtracting the PMIDs that were "un-triaged" to the files triage+train.txt and triage+test.txt.
	ir.ohsu.edu /genomics/2004update.html (1455 words)

	pmns
		The descendent nodes are defined by the set of names, relative to the pathname of their parent non-leaf node.
		The syntax for the pmid specification has been chosen to help manage the allocation of PMIDs across disjoint and autonomous domains of administration and implementation.
		This hierarchic numbering scheme is intended to mirror the implementation hierarchy of performance metric domain, met- rics cluster (data structure or operational similarity) and individual metric.
	www.uni-kiel.de /rz/altix-doc/man_html/man4/pmns.4.html (831 words)

	[No title] (Site not responding. Last check: 2007-11-06)
		After summing all the scores for each paper, the algorithm should rank all the papers by the score, remove the ones already seen in the collection, and report the 5 most related.
		If two scores have a tie in their scores, please report the one with higher PMID (it means the paper is newer and might be more interesting).
		Deliverables (to be submitted online through the course website): Your program source code The best 5 papers’ PMIDs with their scores, using each scoring option.
	www.biostat.harvard.edu /~kbetts/courses/bist280/hw1/HWB1.doc (351 words)

	2004 MEDLINE Documentation - medline04n0418 (Site not responding. Last check: 2007-11-06)
		PMIDs for deleted records had also not been exported during this time and are included in the catch-up files.
		In addition, these records contain <CommentsCorrections>, <RetractionOf>, and <RefSource>, and <PMID> elements, with the citation and PMID of the article being retracted residing in its <RefSource> and <PMID> elements.
		Records for the publications being retracted also contain <CommentsCorrections>, <RetractionIn>, <RefSource> and <PMID> elements, with the citation and PMID of the article citing the retraction residing in its <RefSource> and <PMID> elements.
	www.nlm.nih.gov /bsd/license_doc_notes/med04n0418.html (924 words)

	PLAYGROUND PROJECTS (Site not responding. Last check: 2007-11-06)
		Every PMID has a hyperlink to its corresponding PubMed abstract where one could see the selected words highlighted in the browser.
		This application was intended to generate PMIDs out of reference sections for printed documents such as book chapters that historically do not have PMIDs at the time of the publication but are organized conceptually well.
		Upon submission of plain list of PMIDs; generates two XML files that comply to the CytoScape convention (www.cytoscape.org) engaging Gene Ontology framework (www.geneontology.org) for the generation of conceptual relationships between genes/proteins visually similarly to pathways.
	helga.dyndns.org:808 (279 words)

	[No title]
		List in plain text format (stemcellpapers.txt) of 81,416 PubMed Identifiers (PMIDs) linked to abstracts in MEDLINE that have one or more MeSH terms which are members of the set of terms related to stem cell.
		A zip compressed file (file4.zip) containing lists in plain text format (paperscores-adjectives.txt, paperscores-nouns.txt, paperscores-nounsadjectives.txt, paperscores-verbs.txt) of 81,416 PMIDs of references randomly selected from MEDLINE and their scores according to nouns, adjectives, verbs, and combined nouns/adjectives.
		A zip compressed file (file5.zip) containing a table in plain text format with tab separated columns (paperscores-nouns-recent.txt) of 6,923 PMIDs of references not included in the training set with their scores, and a human evaluation of their relevance to the topic of stem cells.
	www.ogic.ca /projects/ks2004 (188 words)

	Job Details
		The goal of the research is to identify causal relationships between gene-gene or gene-clinical traits and represent them in networks or probabilistic graphic models.
		Such causal networks (PMIDs 15237224, 15965457, 16126366, 16200066) will be used to elucidate disease or drug mechanism, to aid target discovery and target prioritization.
		The responsibilities of this position include developing novel methods for integrating diverse data sources, comparing different networks (such as networks for human and mouse, or liver and adipose) and identifying common features among networks or distinct pathways between normal networks and disease specific networks.
	www.hirehealth.com /Public/JobDetails.aspx?JOB_ID=180982 (272 words)

	2003 Medline Retractions (Site not responding. Last check: 2007-11-06)
		One record that entered MEDLINE, PMID 12557900, is a retraction of publication.
		PMID 10784445: Schon JH, Kloc C, Haddon RC, Batlogg B. Science.
		PMID 11701891: Schon JH, Meng H, Bao Z. Science.
	www.ovid.com /site/support/200301Retractr.html (2229 words)

	MedRefs Medical References Management Database Manual
		The current version of Medrefs requires PMIDs to be positioned as the beginning field of a citation, which is the form found at PubMed (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed) but not currently at the NLM (http://gateway.nlm.nih.gov).
		The references may also be sorted by PMID ("UI"), Reverse PMID ("RevUI"), Title ("TI"), Source ("SO"), First Author ("AU"), Institution ("IN"), Year of Publication ("YR"), and Reverse Year of Publication ("RevYR").
		In addition, sorting by RevYR is optimized to allow the identification of duplicate articles that have been entered once with a custom PMID and subsequently with a an official PubMed PMID, as these unintended duplicates will be found close together.
	www.mcgoodwin.net /pages/medrefs_manual.html (3732 words)

	[No title]
		If the user is interested in registering their service as an Outside Tool, the service must be evaluated before the registration request is submitted.
		If the test is not performed using the most recent set of test PMIDs, the request will be returned for retesting.
		NOTE: If the complete URL created for testing is not listed, or if the PMIDs tested are not the official test PMIDs, the request will be returned. If applicable, a username and password that NCBI staff can use temporarily to view the ILL form.
	support.epnet.com /uploads/kb/registering_openurlbased_services_in_pubmed__summary_sheet.doc (952 words)

	NLPG Resources
		The recovery is based on the PubMed identifier (PMID).
		Required fields have to be inidicated by a parameter in the command line in one string, separated by comma.
		The ranking lenght(number of Pmids) that is to be recovered can be inidicated by a parameter in the command line.
	www.natlang.hcuge.ch /Resources/softs.htm (179 words)

	Announcements to NLM MEDLINE Licensees [29 August 2003] (Site not responding. Last check: 2007-11-06)
		This year the last distribution of new and revised completed records for the 2003 production year will take place early November 2003; the exact date will be announced soon.
		As a reminder, all update files should be processed in ascending numeric order by filename and applied after the baseline files.
		Remember that beginning with the 2004 version of MEDLINE, NLM will no longer export <MedlineID> and the <PMID> will be the only accession number exported to licensees and used in NLM's PubMed®.
	www.nlm.nih.gov /bsd/license_announce/announce_03_aug_29.html (848 words)

	MedRefs and the Chronic Fatigue Syndrome Database
		It is also capable of translating and importing PubMed citation listings starting with the citations in plain text file format.
		Current fields individually stored by MedRefs include PMID (formerly Medline UI), Author, Title, Source, Institution, and Abstract -- certain other fields are stored with the Abstract when the citations are imported.
		As of September 2004, all former Medline UIs have been replaced with PubMed PMIDs.
	www.mcgoodwin.net /pages/medrefs.html (923 words)

	RLIMS-P [PIR - Protein Information Resource]
		The RLIMS-P program is now adopted at PIR and being developed into an online text mining tool for extracting protein phosphorylation information from PubMed literature.
		Enter PubMed IDs (PMIDs) delimited by "," or space, e.g., 2108025, 16436437...
		When input exceeds 100 PMIDs, the process may take up to 1 to 2 minutes.
	pir.georgetown.edu /iprolink/rlimsp (123 words)

	[MOBY-l] PubFetch - MOBY (Site not responding. Last check: 2007-11-06)
		Select the Objects (PMID String) that you want to send and click "Send Selected Objects to Service" You will get the articles in MEDLINE display format in next page I also need some suggestions 1.
		Should I return "PMID" as an Object from the PubMed for given query instead of "String" with "PMID" as Namespace 3.
		I think it is a good idea to register a "PubMed/Medline" object for article returned from PubMed in Medline format.
	open-bio.org /pipermail/moby-l/2003-August/000554.html (295 words)

	[No title]
		Currently, Wormbase curates CGC and PMID papers about C. elegans.
		Below is the description of how PMID papers relevant to C. elegans are selected.
		The list of CGC papers is compiled by CGC and the corresponding protocol is not described here.
	www.its.caltech.edu /~wormbase/CuratorHelp/sop/agp.txt (933 words)

	HELP [PIR - Protein Information Resource]
		Submission of PMIDs as input, returns a summary table for all PMIDs with links to full reports.
		The summary table lists the PMID of each phosphorylation-related abstract along with its top-ranking annotation result, followed by a list of remaining PMIDs for abstracts containing no phosphorylation information.
		Full reports can be retrieved from the summary table using hypertext links (from “text evidence") or by selecting one or more PMID(s) in the list.
	pir.georgetown.edu /pirwww/support/help.shtml (8635 words)

	About Ross Singer's Umlaut [OCLC]
		The goal is to have all of the available information available to that user at hand to draw from, including public libraries or other schools or libraries they have access to.
		If there's a standard identifier (currently just dois and pmids, based on the needs of our population, but there are stubs for oclc numbers, bibcodes and handles), it looks it up against the id authority (crossref, pubmed, etc.) and grabs all of the metadata about the citation from those sources.
		It then takes the metadata, and submit requests to SFX (other link resolvers could be supported, but that's all I have access to), our catalog (which is exported to a Zebra database) and our state union catalog (both searched via SRU).
	www.oclc.org /research/announcements/features/umlaut-about.htm (738 words)

	CBioC : Collaborative Bio Curation from the BioAI Lab at Arizona State University
		New feature: display facts from multiple PMIDs by entering a comma-separated list in the search box.
		You can also display the facts available for a set of abstracts by typing a comma-separated list of their PMIDs in the search box.
		The search box also lets you see all the facts we have from a particular database by typing its name, such as "BIND" or "MINT".
	cbioc.eas.asu.edu /functionality.php (710 words)

	Touro College
		Use PMIDs (PubMed IDs) you find to search Full-Text Periodicals for articles.
		Use any PMIDs (PubMed IDs) you find to search Full-Text Periodicals for articles.
		QUAKELINE - Can search over 44,900 citations & abstracts of journal articles, conference papers, technical reports, etc., back to 1987 on earthquakes, natural hazard mitigation, etc..
	www.touro.edu /Library/sites/BiblioIndex-HealthSciences.asp (2014 words)

	Journals with both Print and Electronic Versions (fwd) (Site not responding. Last check: 2007-11-06)
		DOCLINE libraries, There are some very major journals for which NLM indexes the online version instead of the print equivalent.
		This can cause a problem with DOCLINE requests, since the MEDLINE UIs and PMIDs for articles from these journals point to the online version of the source, not the print version.
		So, for articles from these journals, use the NLM UI for the print version of the journal to generate DOCLINE requests.
	mailman1.u.washington.edu /pipermail/hlib-nw/2001-February/005463.html (390 words)

	Human protein: Q9UCG9 - Urinary gonadotrophin peptide (Fragment). EMBL Bioinformatics Harvester
		This gene was originally thought to be one of the two pseudogenes of the CG beta subunit because it contains a point mutation in the donor splice site (GT -> GA) for the first intron.
		However, two different groups (PMIDs: 1371113 and 8954017) reported identification of a transcript, resulting from alternative splicing of exon 1, capable of encoding a protein of 132 aa.
		The deduced aa sequence of this hypothetical protein does not share any similarity with that of functional CG beta subunits, neither does it correspond to any known protein in the GenBank database.
	harvester.embl.de /harvester/Q9UC/Q9UCG9.htm (555 words)

	PubFetch
		Retrieve the text information from the LitDb corresponding to a supplied accession number (eg.
		Search criteria are passed to Getrefs via the web interface, this returns a list of matching PMIDs from PubMed, these are then checked for duplicates, redundancy, etc. A second method is called in GetRefs.pm that is passed the PMIDs required and retrieves the text record for the desired references.
		This data is converted to a RGD XML format and passed to LoadRefs.pm which parses the reference data and loads it into the appropriate db tables.
	www.gmod.org /nondrupal/pubfetch (482 words)

	[No title]
		The results will provide background and baseline data useful in building and evaluating biomedical information extraction systems.
		Availability and supplementary information: The PMIDs in the corpus used is specified in the long version of this paper, which is at
		The database derived from the corpus is available on request.
	class.ee.iastate.edu /berleant/home/me/cv/papers/corpusproperties.htm (4847 words)

	Stats: Difficulties in generalizing research (February 15, 2006, Evidence, External validity)
		There are three related articles which I might add commentary to in this weblog.
		The PMIDs for these articles are 10797031, 12509644, and 11386894.
		Sorry that I do not even have time to give a full bibliographic citation right now.
	www.childrens-mercy.org /stats/weblog2006/GeneralizingResearch.asp (731 words)

	Third Street Software Forums: Zero references returned for 19 PMIDs
		The daily search was halted because "Zero references returned for 19 PMIDs"
		Re: Zero references returned for 19 PMIDs [Re: silvo]
		This message is normally only seen when there has been some sort of low-level communication error with the data source (e.g., the network dropped, PubMed went down briefly, etc.).
	www.thirdstreetsoftware.com /forums/showflat.php?Cat=0&Number=1848&Main=1840 (149 words)

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