(project) ::: PubTerm - A term-browser alternative for PubMed

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Installation: PUBTERM NEEDS Cross-origin resource sharing (CORS).
Install an extension in Chrome (for example Allow-Control-Allow-Origin).
Install an extension in Firefox
Safari does not seem to work correctly with PubTerm. Please use other browser.
Other browsers? Try! If not working, try installing a CORS extension or another browser.



PubTerm is a tool that help to revise and annotate abstracts from PUBMED organizing them by terms such as genes, diseases, mutations, chemicals, or other user terms.
The first phase is to retrieve abstracts from PUBMED (options 1a or 1b).
Then in options (2) you may configure how and which terms to highlight.
All abstracts can be viewed in option Records (3).
Abstracts organized by genes/disease/chemicals/mutations/species/user terms and others can be viewed in option Term View (4).
Abstracts organized by the co-occurrence of genes/disease/chemicals/mutations/species/terms can be viewed in Co-Occurrence (5).
Abstracts organized by specific words can be viewed in Sentences (6).
Abstracts annotated can be viewed in Annotations (7).



Tutorial of PubTerm

Version 1.1

PubTerm is a 'Term-atic' web tool to assist in the analysis and investigation of large number of PubMed abstracts through automatic annotation and manipulation.

Features:

  • Search PubMed: PubTerm uses PubMed web services to query abstracts. Therefore, the output is exactly the same than using PubMed.
  • Search PubMed from PMID list: Alternatively, if the user 'filter' its own PMID list, it can be feed into PubTerm to perform the analysis.
  • Automatic Annotation: PubTerm uses PubTator (reference) annotations, which contain GENE, DISEASE, CHEMICALS, SPECIES, and MUTATIONS.
  • User Annotation: PubTerm allows user to add own lists of terms.
  • Terms highlighting: Terms are highlighted by colors (either from automatic annotation or from user annotations). Colors can be changed.
  • Abstract Overview: Abstracts can be organized by terms allowing the user to 'focus' its reading in specific abstracts.
  • Abstract Classification: Abstracts can be classified by user terms. This allows the user to 'mark' abstract in categories for further analysis or reference.
  • Abstract highlights/marks: Abstracts can be marked to highlight text or important information.
  • Abstract Notes: Abstracts can be annotated with text notes.
  • Term Notes: Terms (PubTator annotations such genes, disease, etc.) can be annotated with text notes for further analysis and manipulation.
  • Term Classification: Terms (PubTator annotations such genes, disease, etc.) can be classified by user terms. This allows the user to 'mark' terms in categories for further analysis or reference.
  • Print/Export: Data can be printed/exported to CSV, Excel, PDF, or to device clipboard by using the proper buttons in tables.
  • Session saving/restoring: Your work can be saved or restored in the PubTerm server (it depends on the availability of our server).
Step 1 - Specify your PUBMED search:


Step 2 - Specify the amount of abstracts for analysis:


Step 3 - If results > 100, click 'Retrieve' to confirm:



Note: Abstract download depends on your Internet connection and PubMed service. Annotations depends on PubTerm service.
Step 1: Paste below the list of PMIDs (PubMed Id's) to be analyzed (an example is provided for reference).

Note: Text can be delimited by "," or ";" or lines. Everything rather than numbers are removed. PMCIDs are not accepted and will be removed. Basically you can select your abstracts in PubMed the way you like and export them to CSV then open the file in a spreedsheet program like Excel or OpenOffice/LibreOffice then paste the column "Identifiers".

Step 2:


Note: Abstract download depends on your Internet connection and PubMed service. Annotations depends on PubTerm service.
RecordsColorsTerms
Customizable User Terms 1 or Categories 1:

Customizable User Terms 2 or Categories 2:

Customizable User Terms 3 or Categories 3:


Customizable terms in lines. Separate synonyms or similar words with a vertical bar |.
Session Information
Id/Keyword
e-Mail
Project


No passwords are asked or saved.
The Id/Keyword field can be used to specify a secret word.
We do not use or share e-mail accounts and are not checked for validity.
Session Information
Id/Keyword
e-Mail
Project


Project is optional. If left blank a list of sessions associated to the Id and e-Mail will be shown.
Session Information
Id/Keyword
e-Mail
Project
Restore Marks
Restore Notes
Restore Categories
Restore Used
Restore Term Notes
Restore Term Categories
Only empty recordsAdd categories and notes only for those records (terms/abstracts) that are empty.

Wellcome to PubTerm Tool

PubTerm is a 'Term-atic' web tool to assist in the analysis and investigation of large number of PubMed abstracts through automatic annotation and manipulation.

Features:

  • Search PubMed: PubTerm uses PubMed web services to query abstracts. Therefore, the output is exactly the same than using PubMed.
  • Search PubMed from PMID list: Alternatively, if the user 'filter' its own PMID list, it can be feed into PubTerm to perform the analysis.
  • Automatic Annotation: PubTerm uses PubTator (reference) annotations, which contain GENE, DISEASE, CHEMICALS, SPECIES, and MUTATIONS.
  • User Annotation: PubTerm allows user to add own lists of terms.
  • Terms highlighting: Terms are highlighted by colors (either from automatic annotation or from user annotations). Colors can be changed.
  • Abstract Overview: Abstracts can be organized by terms allowing the user to 'focus' its reading in specific abstracts.
  • Abstract Classification: Abstracts can be classified by user terms. This allows the user to 'mark' abstract in categories for further analysis or reference.
  • Abstract highlights/marks: Abstracts can be marked to highlight text or important information.
  • Abstract Notes: Abstracts can be annotated with text notes.
  • Term Notes: Terms (PubTator annotations such genes, disease, etc.) can be annotated with text notes for further analysis and manipulation.
  • Term Classification: Terms (PubTator annotations such genes, disease, etc.) can be classified by user terms. This allows the user to 'mark' terms in categories for further analysis or reference.
  • Print/Export: Data can be printed/exported to CSV, Excel, PDF, or to device clipboard by using the proper buttons in tables.
  • Session saving/restoring: Your work can be saved or restored in the PubTerm server (it depends on the availability of our server).
Fields:
     Select:      ><     
   
Fields:
           
View Rows by: having occurrences
View Columns by: having occurrences
><     Data Table Mode:     

           
Size:   Within:

Status