Papers Page Code

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(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:

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):

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

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> "", also "URL: <A HREF=></A>" in <html> section.

category labid title website html
Research GrantsdonDongahue Young Investigator 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=></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. grab googlespreadsheet with python, see Grab_GoogleSpreadsheet_with_a_Python
Other Code: see PubmedSpreadsheet_Generation_Code


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

  • 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: : 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

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),]
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