Outline Application one.
How to get related literature from PubMed? To store search results in database and find query
keyword.
Application two. How to establishment your own dictionary?
Application three. How to search detail information, like TF-TF relations
et al.
Application four. To construct co-occurrence graph.
Application one cont. Practice.
To get related literature that you want to known in XML data format by using PubMed web service in NCBI website. (like E2F1, ERE et al.)
Advanced exercise. To get sequence data from PubMed. To establish sequence database by using Perl and
MySQL.
Application one cont. What Perl language need?
Some Perl packages. Known data (input data).
User query keyword, like “Estrogens”.
Information (output data). Query results, like “Estrogens related candidate data”.
Knowledge (related data). Data mining (extraction) from related candidate data.
Information KnowledgeData Sets
Application one cont.
Information
User Query
PubMed Online Database
Output File
User want to know
Download onlineService from PubMed
Candidate relatedLiteratures
Output file of XML data
Application one cont. To store search results.
XML File
MySQL Database
Data Analysis
Literature data (PMID, Year et.al)
XML format dataof query results
Data analysis forpreparing to store data
Query results inMySQL Database
Application one cont. Practice.
To store obtained data into MySQL database. PMID Journal name Article Title Abstract PubDate
Application one cont. To find query keyword.
All Literatures
MySQL Database
Tagged ResultsWeb Page
Tagging
User Query
Query Keyword
Tagging keyword
All Literatures inMySQL Database
Tagging All LiteraturesAccording to Keyword
Displaying TaggedResults by Web Page
Application one cont. Practice.
Tagging related abstracts from candidate literatures. Gene name or protein name. Action words.
Application one cont. Challenge.
A tagging program that include two query words. Query word one.
Tagged abstracts. Un-tagged abstracts.
Query word two. Tagged abstracts. Un-tagged abstracts.
Complete data extraction system.
Get Related Literatures from PubMed
Store Related Literatures into Database
Find Some Information from Text File or Database
Application two To establish transcription factor (TF)
dictionary. From EBI-SRS online resource.
To get TF text data from EBI-SRS. Using Perl language to extract some data. To store data into MySQL by Perl language.
操作示範
Practice.
Application three To search TF-TF relations from established
literatures. Using TF dictionary. Using Perl language to extract co-occurrence
relations.
操作示範
Practice.