Can I optimize the extraction of information from PubMed with MedScan using the Plant Cartridge?

As the proportion of abstracts related to Plant in PubMed is low, it is worthwhile to use the advanced search options available in PubMed to enrich for plant references when performing a PubMed search in MedScan. You can incorporate limits – i.e. specify a list of journals related to Plant biology in the ‘Search by Journal’ section (Figure 1). This will help to reduce false positive extraction facts from articles related to human and mouse. 

Depending on the MedScan search option, the procedure of optimization is different:

- Search PubMed (extract up to 500 abstracts in one search; Figure 2 red arrow):  
1. Directly via the MedScan interface, click on the ‘limits’ tab from the PubMed homepage to access advanced search options.
2. From this page you can incorporate limits on selected journals.
3. Click on ‘Go’ to run your optimized query 

- Quick Import > Import PubMed dataset (extract up to 1000 abstracts;  Figure 2 blue arrow):
1. Open the PubMed homepage (http://www.ncbi.nlm.nih.gov/pubmed/) in your favorite web-browsner.
2. Click on the ‘limits’ tab from the PubMed homepage to access advanced search options.
3. From this page you can incorporate limits on selected journals.
4. Click on ‘Go’ to run your optimized query
5. Copy (Ctrl+C) the optimized query that is displayed in the text box
6. Go back to the MedScan Reader interface
7. Paste (Ctrl+V) the clipboard content in the text box beside ‘Import PubMed dataset’ in the ‘Quick Import’ section.
8. Click on ‘Query and Import’ to run your optimized query 

- Import Relations from Literature via MedScan (extract up to 10000 abstracts; Figure 3)
1. Follow step 1 to 5 of the previous section
2. Go to the Pathway Studio interface
3. From the Home tab, click on the import button and choose the option ‘Import Relations from Literature via MedScan®…’ in the drop down menu.
4. Paste (Ctrl+V) the clipboard content in the text box beside ‘PubMed query’ in the section ‘Search PubMed and process text from retrieved abstracts’.
6. Name the new pathway containing imported relations in the text box 'Pathway name'
5. Click on ‘Start’ to run your optimized query. Imported relations are added to the opened ResNet database and collected into a new pathway.