Papers Page Code

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==Word Cloud==
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==New Stuff==
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Link to [[Word Cloud]]
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[https://docs.google.com/spreadsheet/ccc?key=0AiiHlTECOi8edGhzSXlZZzEyRThQeDB6R0pRc0FvcGc&hl=en_US#gid=0 MBGLab--Papers-Master]  
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== (Lab Member) Papers Page Rebuild and Further Info (Private)==
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*Private Wiki includes instructions about how to update papers page and further info, click here [http://wiki.gersteinlab.org/labinfo/Papers_Page_Documentation Private Wiki]
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[https://docs.google.com/spreadsheet/ccc?key=0AiiHlTECOi8edDBCUUhtMFZzRFVMaVlxZ1JrNGp1b0E&hl=en_US#gid=0 Papers-Subjects]
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==Papers GitHub==
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Papers 2.0 is now version controlled under GitHub: https://github.com/gersteinlab/papers.gersteinlab.org
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==Automatic generation of publication documents from SpreadSheet==
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==SpreadSheet Structure==
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*"Papers Page" is built up from two basic google spreadsheets, "Papers Master" and "Papers Subjects". "Papers Master" contains descriptions about papers, such as, pubmed ID, authors, citation, et al..  Papers are affiliated to some grants. Grants information is stored in "Papers Subjects".
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Here is a list of the tags and their meanings<br \>
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===Papers Master===
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Papers Master:
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<labid> - id by which to refer to the article
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<PMID> - PubMed id
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<title> - title of the article
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<citation> - citation of the article (author, journal, year, etc)
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<preprint> - URL of the preprint file
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<subjects> - specifies the grant(s) funding the paper (e.g. "cegs,keck")
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<website> - supplemental website
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<Year> - year the article was published
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<footnote> - additional information
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<website2> - second supplemental website
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====[http://papers.gersteinlab.org Return to index]====
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The tags can conceptually be divided into two groups: ones such as PMID and title, which serve to identify the paper, and tags such as website and subject which supply supplemental information about the paper. There are two ways to identify a paper (in order of decreasing precedence):
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I. PMID<br \>
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II. title, citation
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<font size="3" face="arial, Helvetica, sans-serif"> '''Introduction and guidelines:''' All papers are defined by a unique "labid" such as "pgenes-nar" or "genome-transposon-nature". Ideally, the labid should contain the abbreviated subject and journal name as shown. To add a paper, you simply need to go to MBGLab--Papers-Master (Link above) , then fill in the corresponding columns. If you also want to add a new subject area, go to Papers-Subjects (Link above). After finishing adding new papers, go to [http://wiki.gersteinlab.org/labinfo/Main_Page Private Wiki] and find the rebuild link (under Papers / Manuscripts ), then click it.  
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You should always include the PMID if a paper is known to be listed in PubMed. Option 2 should be used for papers that are in press.
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Here is a list of the tags and their meanings:
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The other group of tags supplies additional information about the paper specified by the first group of tags. All of these tags are optional, however used of <subjects> and <preprint> is strongly encouraged.
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<blockquote>
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{| border="1" cellpadding="0" cellspacing ="0"
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*Papers Master
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! scope="col" width="50" align="center" style="background:#f0f0f0;"|'''labid'''
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<Labid> - id by which to refer to the article <br />
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! scope="col" width="50" align="center" style="background:#f0f0f0;"|'''PMID'''
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<PMID> - PubMed id<br />
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! scope="col" width="50" align="center" style="background:#f0f0f0;"|'''title'''
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<Title> - title of the article (If pubmed id exists, leave blank) <br />
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! scope="col" width="50" align="center" style="background:#f0f0f0;"|'''citation'''
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<Citation> - citation of the article (author, journal, year, etc) (If pubmed id exists, leave blank)<br />
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! scope="col" width="50" align="center" style="background:#f0f0f0;"|'''preprint'''
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<preprint> - URL of the preprint file<br />
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! scope="col" width="50" align="center" style="background:#f0f0f0;"|'''subject'''
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<subjects> - specifies the grant(s) funding the paper (e.g. "cegs,keck") (refer to Papers Subjects)<br />
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! scope="col" width="50" align="center" style="background:#f0f0f0;"|'''website'''
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<website> - supplemental website<br />
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! scope="col" width="50" align="center" style="background:#f0f0f0;"|'''Year'''
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<Year> - published year of an article (must fill in) <br />
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! scope="col" width="50" align="center" style="background:#f0f0f0;"|'''footnote'''
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<footnote> - footnote of this article <br />
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! scope="col" width="100" align="center" style="background:#f0f0f0;"|'''website2'''
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<website2> - second supplemental website<br />
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|-
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*Papers Subject
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|metamembrane||20430783||||||http://archive.gersteinlab.org/papers/e-print/metamembrane/preprint.pdf||interactions||http://metagenomics.gersteinlab.org/membrane||2010||||||
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<Category> - classification of research areas<br />
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|}
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<LabID> -name of grants <br />
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<Title> - brief description of grants <br />
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<Website> - website of research grants <br />
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<Html> - content appears on webpage <br />
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</blockquote>
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The tags can conceptually be divided into two groups: ones such as PMID and labitle, which serve to identify the paper, and tags such as website and subject which supply supplemental information about the paper. There are two ways to identify a paper (in order of decreasing precedence):
 
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# PMID
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Spreadsheet of Paper IDs and PubMed IDs with other annotation: MBGLab--Papers-Master ([https://docs.google.com/spreadsheet/pub?hl=en_US&hl=en_US&key=0AiiHlTECOi8edGhzSXlZZzEyRThQeDB6R0pRc0FvcGc&output=html HTML]) ([https://docs.google.com/spreadsheet/pub?hl=en_US&hl=en_US&key=0AiiHlTECOi8edGhzSXlZZzEyRThQeDB6R0pRc0FvcGc&output=csv CSV])
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# Title, Citation
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You should always include the PMID if a paper is known to be listed in PubMed. Option 2 should be used for papers that are in press.
+
===Papers Subjects===
 +
Papers Subjects:
 +
<category> - classification of grants
 +
<labid> - id refer to each grant
 +
<title> - description of each grant
 +
<website> - external website
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<html> - additional information
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The other group of tags supplies additional information about the paper specified by the first group of tags. All of these tags are optional, however used of <tt><subjects></tt> and <tt><preprint> </tt> is strongly encouraged. (Please consult Mark for guidelines on citing grants.)
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We encourage you to sort <category> after adding new grants because of coding issues. <website> should also be reflected in <html> section. For example, "don" has <website> "http://www.donaghue.org", also "URL: <A HREF=http://www.donaghue.org> http://www.donaghue.org</A>" in <html>  section.
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</font>
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==Rebuild Link==
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{| border="1" cellpadding="0" cellspacing ="0"
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{|
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! scope="col" width="50" align="center" style="background:#f0f0f0;"|'''category'''
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|[http://wiki.gersteinlab.org/labinfo/Main_Page Rebuild Link on private wiki]
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! scope="col" width="50" align="center" style="background:#f0f0f0;"|'''labid'''
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| align="center" |
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! scope="col" width="50" align="center" style="background:#f0f0f0;"|'''title'''
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! scope="col" width="50" align="center" style="background:#f0f0f0;"|'''website'''
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! scope="col" width="50" align="center" style="background:#f0f0f0;"|'''html'''
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|-
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|Research Grants||don||Dongahue Young Investigator||http://www.donaghue.org/||Young investigator award from Donaghue Foundation to M Gerstein (PI), "Comparative Genomics of Microbial Pathogens," (DF98-113, 1/1/99-12/31/03). URL: <A HREF=http://www.donaghue.org> http://www.donaghue.org</A>Articles funded by this grant:
|}
|}
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==Old Code Page==
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[https://docs.google.com/spreadsheet/pub?key=0AiiHlTECOi8edDBCUUhtMFZzRFVMaVlxZ1JrNGp1b0E&output=html HTML table of all subject headings in the current papers page]
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Redirect [[Papers Page Code Old]]
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===MBGLab--Papers XML Import===
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[https://docs.google.com/spreadsheet/pub?key=0AiiHlTECOi8edHFxQWRwN0kxeTQ3ZzdCOXhQX2Z1ZGc&output=html HTML table of all PubMed entries in tabular format]
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==Generate publication documents from SpreadSheet==
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Two Steps Flowchart (created by Mike Wilson):
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[[Image:Papers1.png||Import XML Flow]] &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; [[Image:Papers2.png||Rebuild Papers Page]]
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* Download XML file from NCBI using PubMed ID to generate pubmed_spreadsheet. Pubmed_spreadsheet stores <title> <citation> et al. of papers corresponding to "PMID" in "Papers Master". This step is done by scripts automatically.
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GoogleSpreadsheet.py: grab googlespreadsheet with python, see [[Grab_GoogleSpreadsheet_with_a_Python]]<br \>
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Other Code: see [[PubmedSpreadsheet_Generation_Code]]
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Pipeline:
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First obtain pubmed_result.xml from papers medline query
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    parse_pmids.py<br \>  curl `cat ncbiquery.txt` > NCBIData.xml
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Reformat NCBIData.xml to tab delimited file to upload to Google
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    python import.py
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replace PubMed Import XML spreadsheet with export_out.tab
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    reload_data.py
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*Build Papers Page
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This step grabs all information from three spreadsheets, "Papers Master","Papers Subjects" and "Pubmed_Spreadsheet", to build up the whole website. Each paper and each grant has its own description page.
 +
 
 +
Script used in this step:
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update.py : see [[Build_Papers_Page_Code]]
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==Papers Page Code (Old)==
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*[[Papers_Page_Code_Old]]
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==Old Papers Server ... and also R code for NSF colab ==
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*Old version of pagers website  [http://oldpapers.gersteinlab.org Old Papers]
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*Other info of papers [[Paper_search]]
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R Code for compiling list of NSF co-authors:
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This is buggy and approximate, but a good place to start
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https://github.com/ejfertig/NSFBiosketch/blob/master/CollaboratorList.Rmd
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library('easyPubMed')
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library('plyr')
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library('xlsx')
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author <- 'Gerstein M'
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authorFilter <- 'Gerstein Maya'
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currentDate <- Sys.Date()
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queryDate <- seq(Sys.Date(), length = 2, by = "-48 months")[2]
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pmquery <- sapply(articles_to_list(fetch_pubmed_data(get_pubmed_ids(paste0(author,'[Author]')))),article_to_df)
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names(pmquery) <- NULL
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pmquery <- pmquery[sapply(pmquery,function(x){any(colnames(x)=='year')})]
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datePMID <- as.Date(sapply(pmquery,function(x){paste(x[1,'year'], x[1,'month'], x[1,'day'],sep="-")}))
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pmquery <- pmquery[datePMID >= queryDate]
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pmquery.dataframe <- ldply(pmquery,data.frame)
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pmquery.dataframe$Initials <- getInitials(pmquery.dataframe$firstname)
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pmquery.dataframe$ColabType <- 'Co-Author'
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pmquery.dataframe <- pmquery.dataframe[!duplicated(paste(pmquery.dataframe$lastname,pmquery.dataframe$Initials)),]
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pmquery.dataframe <- pmquery.dataframe[order(pmquery.dataframe$lastname,pmquery.dataframe$Initials),]

Latest revision as of 17:02, 16 September 2019

Contents

Word Cloud

Link to Word Cloud

(Lab Member) Papers Page Rebuild and Further Info (Private)

  • Private Wiki includes instructions about how to update papers page and further info, click here Private Wiki

Papers GitHub

Papers 2.0 is now version controlled under GitHub: https://github.com/gersteinlab/papers.gersteinlab.org

SpreadSheet Structure

  • "Papers Page" is built up from two basic google spreadsheets, "Papers Master" and "Papers Subjects". "Papers Master" contains descriptions about papers, such as, pubmed ID, authors, citation, et al.. Papers are affiliated to some grants. Grants information is stored in "Papers Subjects".

Here is a list of the tags and their meanings

Papers Master

Papers Master: 

<labid> - id by which to refer to the article
<PMID> - PubMed id
<title> - title of the article
<citation> - citation of the article (author, journal, year, etc)
<preprint> - URL of the preprint file
<subjects> - specifies the grant(s) funding the paper (e.g. "cegs,keck")
<website> - supplemental website
<Year> - year the article was published
<footnote> - additional information
<website2> - second supplemental website

The tags can conceptually be divided into two groups: ones such as PMID and title, which serve to identify the paper, and tags such as website and subject which supply supplemental information about the paper. There are two ways to identify a paper (in order of decreasing precedence):

I. PMID
II. title, citation

You should always include the PMID if a paper is known to be listed in PubMed. Option 2 should be used for papers that are in press.

The other group of tags supplies additional information about the paper specified by the first group of tags. All of these tags are optional, however used of <subjects> and <preprint> is strongly encouraged.

labid PMID title citation preprint subject website Year footnote website2
metamembrane20430783http://archive.gersteinlab.org/papers/e-print/metamembrane/preprint.pdfinteractionshttp://metagenomics.gersteinlab.org/membrane2010


Spreadsheet of Paper IDs and PubMed IDs with other annotation: MBGLab--Papers-Master (HTML) (CSV)

Papers Subjects

Papers Subjects: 

<category> - classification of grants
<labid> - id refer to each grant
<title> - description of each grant
<website> - external website
<html> - additional information

We encourage you to sort <category> after adding new grants because of coding issues. <website> should also be reflected in <html> section. For example, "don" has <website> "http://www.donaghue.org", also "URL: <A HREF=http://www.donaghue.org> http://www.donaghue.org</A>" in <html> section.

category labid title website html
Research GrantsdonDongahue Young Investigatorhttp://www.donaghue.org/Young investigator award from Donaghue Foundation to M Gerstein (PI), "Comparative Genomics of Microbial Pathogens," (DF98-113, 1/1/99-12/31/03). URL: <A HREF=http://www.donaghue.org> http://www.donaghue.org</A>Articles funded by this grant:

HTML table of all subject headings in the current papers page

MBGLab--Papers XML Import

HTML table of all PubMed entries in tabular format

Generate publication documents from SpreadSheet

Two Steps Flowchart (created by Mike Wilson):

Import XML Flow              Rebuild Papers Page

  • Download XML file from NCBI using PubMed ID to generate pubmed_spreadsheet. Pubmed_spreadsheet stores <title> <citation> et al. of papers corresponding to "PMID" in "Papers Master". This step is done by scripts automatically.

GoogleSpreadsheet.py: grab googlespreadsheet with python, see Grab_GoogleSpreadsheet_with_a_Python
Other Code: see PubmedSpreadsheet_Generation_Code

Pipeline: 

First obtain pubmed_result.xml from papers medline query
   parse_pmids.py
   curl `cat ncbiquery.txt` > NCBIData.xml
Reformat NCBIData.xml to tab delimited file to upload to Google
   python import.py
replace PubMed Import XML spreadsheet with export_out.tab
   reload_data.py


  • Build Papers Page

This step grabs all information from three spreadsheets, "Papers Master","Papers Subjects" and "Pubmed_Spreadsheet", to build up the whole website. Each paper and each grant has its own description page.

Script used in this step:

update.py : see Build_Papers_Page_Code

Papers Page Code (Old)

Old Papers Server ... and also R code for NSF colab

R Code for compiling list of NSF co-authors: This is buggy and approximate, but a good place to start

https://github.com/ejfertig/NSFBiosketch/blob/master/CollaboratorList.Rmd 

library('easyPubMed')
library('plyr')
library('xlsx')
author <- 'Gerstein M'
authorFilter <- 'Gerstein Maya'
currentDate <- Sys.Date()
queryDate <- seq(Sys.Date(), length = 2, by = "-48 months")[2]
pmquery <- sapply(articles_to_list(fetch_pubmed_data(get_pubmed_ids(paste0(author,'[Author]')))),article_to_df)
names(pmquery) <- NULL
pmquery <- pmquery[sapply(pmquery,function(x){any(colnames(x)=='year')})]
datePMID <- as.Date(sapply(pmquery,function(x){paste(x[1,'year'], x[1,'month'], x[1,'day'],sep="-")}))
pmquery <- pmquery[datePMID >= queryDate]
pmquery.dataframe <- ldply(pmquery,data.frame)
pmquery.dataframe$Initials <- getInitials(pmquery.dataframe$firstname)
pmquery.dataframe$ColabType <- 'Co-Author'
pmquery.dataframe <- pmquery.dataframe[!duplicated(paste(pmquery.dataframe$lastname,pmquery.dataframe$Initials)),]
pmquery.dataframe <- pmquery.dataframe[order(pmquery.dataframe$lastname,pmquery.dataframe$Initials),]
Retrieved from "https://info.gersteinlab.org/Papers_Page_Code"
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