PESCADORPlatform for Exploration of Significant Concepts AssociateD to co-Occurrences Relationships.
REFERENCE: PESCADOR, a web-based tool to assist text-mining of biointeractions extracted from PubMed queries. BMC Bioinformatics. 2011 Nov 9;12(1):435
Literature submission (required)
1 Go to the PESCADOR home page at http://cbdm.mdc-berlin.de/~pescador/
2 Choose an input type to provide the PubMed IDs (PMIDs) list to be analysed
A) Use the file upload box
i) Locate in the file system of your computer the text file containing a list of PMIDs. Optionally, you can generate this file from NCBI’s Entrez as explained in the next steps.
ii) Go to http://www.ncbi.nlm.nih.gov/pubmed
iii) Perform a usual query to PubMed
iv) Click on the send to link and select destination File, and format PMID list
B) Use the text area
i) Copy and paste a list of PMIDS.
C) Input a PMID list from another tool
i) Currently implemented in Medline Ranker8 and XplorMed9.
D) Use an example
i) Click on the ‘Example’ link at the bottom of the text area.
CRITICAL STEP: Use a one per line list of PMIDs for the inputs explained above (currently limited to a maximum of 500 PMIDs).
Indicate default Gene Dictionary (required)
3 Type the NCBI Taxonomy ID (TAXID) of the organism where the gene terms should be used (e.g. 9606 for Homo sapiens). You can check at http://www.ncbi.nlm.nih.gov/Taxonomy/ to find the TAXID of your preferred organism.
Skip the Concepts check-up (optional)
4 Click on the link ‘Go to submit’.
Indicate Concept Dictionary (optional)
5 Indicate which words should be used by PESCADOR as a ‘Concept Dictionary’; this might done in two ways
A) Use MeSH vocabulary as “Concept Dictionary”
i) Mark ‘All MeSH terms’ check box. Or
ii) Mark one or more ‘MeSH’ subcategories.
B) Create a customized “Concept Dictionary”
i) Copy/paste or write a one per line list of particular words/sentences in the ‘Customized concepts’ text area (e.g. “aggregation”, “cleavage”).
Submit a project to PESCADOR (required)
6 Push the button ‘Start Analysis’.
Wait for PESCADOR to execute your project
7 Wait for PESCADOR analysis to be concluded. At this Step you can:
A) For small literature searches (up to 100 PMIDs)
i) Follow the conclusion of the four individual steps performed by PESCADOR, or
B) For big literature searches (more than 100 PMIDs)
i) Save the ‘Project ID’ attributed to your project, and load it later in the ‘Retrieval field’ at PESCADOR’s home page when the processing is concluded. Note that the most time consuming step is the tagging and this takes about one second per abstract. Alternatively, you can bookmark this page on your browser and come back later.
8 Click on the link ‘HERE’ to access the results summary of your project.
Visualize the results summary of your project
9 Click on the desired sessions to access individual results. At this step you can:
A) Browse the results of your analysis.
i) Click on the individual links for the report pages (see Steps 10-31).
B) Download the files for the individual results.
Access the “Term Report” page
10 Access “Terms Report Page” by clicking on the link ‘Terms’ in the top menu.
11 Select a gene symbol/synonym on the list available in the left side of the page.
12 Read the “Gene Report Table” for your selected term. Ambiguous terms that appear as symbol/synonym of different GeneIDs are assigned to all GeneID entries (see highlighted terms).
13 Read the “Term Co-occurrence Table” for your selected term. At this step you can:
A) Filter the “co-occurrence types” to be displayed
i) Click on the links ‘1-4’ in the first column of the table to show co-occurrences of type i or better (clicking on type 4 displays all co-occurrence types).
B) Filter the “partner” to be displayed
i) Click on the name of a partner of the selected term in the second or third columns and only co-occurrence with this partner will be displayed.
ii) Click on the link ‘Show All’ above this table to remove this filter.
C) Filter the “biointeraction term” to be displayed
i) Click on the desired ‘biointeraction term’ of the fifth column to display co-occurrences where this term has been found.
ii) Click on the link ‘Show All’ within the heading of this column to remove this filter.
D) Access the abstracts where the co-occurrence has been filtered by clicking on the PMIDS on the seventh column (see Steps 21-25).
14 Visualize the “Term Co-occurrence Network” for your selected term. At this step by clicking on the corresponding buttons above the network you can:
A) Filter the interaction type of edges displayed in the network.
B) Display only edges which have been manually validated (see Step 25).
C) Display the biological concepts found in the co-occurrence analysis as nodes of the network.
D) Reset the network to its default visualization mode.
15 Customize the network display. By clicking on the MEDUSA applet control buttons you can:
A) Select the option ‘Relax’ to relax the network edges.
B) Unselect the option ‘Edge colours’ to remove colours from network.
C) Unselect the option ‘Labels’ to erase the label of the nodes from the graph.
D) Select an option on the ‘Layout’ menu, to change the network topology.
E) Select a method on the ‘Clustering’ menu, to cluster the nodes on the network.
16 Download the network source file by clicking in the link ‘Download’ at the bottom of the network.
Access the “Concept Report” page
17 Access “Concept Report Page” by clicking on the link ‘Concepts’ in the top menu.
18 Select a gene concept on the list available in the left side of the page.
19 Read the “Concept Co-occurrence Table” for your selected term (as explained in Step 13).
20 Download the network source file as explained in Step 16.
Read the abstracts where the co-occurrences have been retrieved.
21 Access “Abstracts Report Page” by clicking on the link ‘Abstracts’ in the top menu.
22 Select a PMID on the list available in the right side of the page.
23 Read the selected sentence-separated abstract with the informative sentences highlighted in green.
24 Check the informative terms on the sentences: biological terms (violet), biointeractions (orange), biological concepts (blue).
25 Read the “Term Co-occurrence Table” for your selected abstract. At this step you can:
A) Click on a name pair on the third or fourth columns to go to the corresponding “Term Report Page” (see Steps 10-16).
B) Validate a suggested pair of this table by clicking on the green ‘Validate’ button on the seventh column.
C) Remove a previously validated pair by clicking on the red ‘Remove’ button on the seventh column.
Visualize the “Global Network Page” for your text mining analysis.
26 Access “Global Network Page” by clicking on the link ‘Network’ in the top menu.
27 Control the displayed network as explained in Steps 14 and 15.
28 Access a biological term or concept report by clicking on the corresponding left side lists.
Manage your validations.
29 Access the “Validations Management Page” by clicking on the link ‘Validations’ in the top menu.
30 Download the current ‘Validation Table’ as a ‘validation tab-delimited text file’ by clicking on the link ‘Download’. This file can be loaded for future projects as a validation table.
31 Manage your “Validation table”, at this Step you can:
A) Add a previously saved ‘validation tab-delimited text file’ to the current ‘Validation Table’ by clicking on the link ‘Load’ and selecting the corresponding file in your computer’s file system. Finally, click on the green button ‘Upload validations’.
B) Clear your current ‘Validation Table’ by clicking on the link clear and then on the red button ‘Remove’.
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