Papers Page Code
From GersteinInfo
(→Generate publication documents from SpreadSheet) |
(→Generate publication documents from SpreadSheet) |
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* Download XML file from NCBI using PubMed ID to generate pubmed_spreadsheet. This step is done by scripts automatically. | * Download XML file from NCBI using PubMed ID to generate pubmed_spreadsheet. This step is done by scripts automatically. | ||
GoogleSpreadsheet.py : grab googlespreadsheet with python, see [[Grab_GoogleSpreadsheet_with_a_Python]] | GoogleSpreadsheet.py : grab googlespreadsheet with python, see [[Grab_GoogleSpreadsheet_with_a_Python]] | ||
| + | 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 | ||
| + | (this can be added to the bottom of PubmedHandler.py instead of exporting the export.tab file using the NewGoogleSpreadsheet.py API) | ||
==Rebuild and Further (private) Info== | ==Rebuild and Further (private) Info== | ||
Revision as of 10:58, 16 September 2011
Contents |
SpreadSheet Structure
- "Papers Page" is generated from two google spreadsheets, "Papers Master" and "Papers Subjects". "Papers Master" stores basic information about each paper. "Papers Subjects" stores information about each grant.
Here is a list of the tags and their meanings:
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. (Please consult Mark for guidelines on citing grants.)
| labid | PMID | title | citation | preprint | subject | website | Year | footnote | website2 | |
|---|---|---|---|---|---|---|---|---|---|---|
| metamembrane | 20430783 | http://archive.gersteinlab.org/papers/e-print/metamembrane/preprint.pdf | interactions | http://metagenomics.gersteinlab.org/membrane | 2010 |
Papers Subjects: <category> - classification of grants <labid> - name 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 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: |
Generate publication documents from SpreadSheet
Two steps:
- Download XML file from NCBI using PubMed ID to generate pubmed_spreadsheet. This step is done by scripts automatically.
GoogleSpreadsheet.py : grab googlespreadsheet with python, see Grab_GoogleSpreadsheet_with_a_Python
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
(this can be added to the bottom of PubmedHandler.py instead of exporting the export.tab file using the NewGoogleSpreadsheet.py API)
Rebuild and Further (private) Info
http://wiki.gersteinlab.org/labinfo/Papers_Page_Documentation
Old Code Page
Redirect Papers Page Code Old
