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PubSearch projects include algorithm and database based search patterns for various industries, we have also created search projects based similar concept of google algorithm which is popular for search engine optimisation or SEO among various search based companies.
PubSearch is a literature curation management system designed to store and manage the available literature for an organism or system of interest. It provides database curators with a powerful literature search capability, stores relevant biological information, creates automatic associations between the biological information and the literature, and provides a user-friendly web interface for manual validation and curation. PubSearch is based on a simple MySQL relational database for the back-end, and Java Servlet and Java Server Pages for the API and front-end applications. PubSearch is extensible, allowing new biological objects of interest to be added, and flexible, allowing programming of different curation strategies. It is currently used for curating biological information for the model organism database for Arabidopsis thaliana, TAIR. The system can be easily adapted for extracting and curating information from the literature for any model organism database. PubSearch is one of the Generic Model Organism Database (GMOD) toolkits and is freely available from the GMOD site.
PubSearch is a literature curation management system designed to store and manage the available literature for an organism or system of interest. It provides database curators with a powerful literature search capability, stores relevant biological information, creates automatic associations between the biological information and the literature, and provides a user-friendly web interface for manual validation and curation. PubSearch is based on a simple MySQL relational database for the back-end, and Java Servlet and Java Server Pages for the API and front-end applications. PubSearch is extensible, allowing new biological objects of interest to be added, and flexible, allowing programming of different curation strategies. It is currently used for curating biological information for the model organism database for Arabidopsis thaliana, TAIR. The system can be easily adapted for extracting and curating information from the literature for any model organism database. PubSearch is one of the Generic Model Organism Database (GMOD) toolkits and is freely available from the GMOD site.
The PubSearch database is the central component of the PubSearch system. The following operations are performed during PubSearch use: Step 1: The PubSearch database is loaded in batch mode using input from other databases such as literature databases (PubMed, Agricola, etc), TAIR (an example model organism database), and the Gene Ontology database. Step 2: The PubSearch database indexes the information by populating the Hit table. Step 3: Through the Java API and the web-interface, curators search, update, validate and insert information, relying on the indexed data in the database. Step 4: Finally, the data is exported to the TAIR production database and other databases such as the Gene Ontology database.
PubFetch is part of the PubSearch web-based literature curation toolset and functions as the interface between the literature curation tools and the online literature databases, such as PubMed. The aim of PubFetch is to provide a generic way of searching and retrieving literature data from online literature datasources so that the downstream applications dont have to deal with the idiosyncracies of the individual literature databases. Initially PubFetch will act as the interface between PubSearch and the PubMed and Agricola databases used by RGD and TAIR. A standard API and data format will be created to provide database queries and return results, popular existing formats and protocols will be used/supported wherever possible.
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The fundamental actions required of PubFetch are as follows:
This is the procedure folliwed by the existing RGD modules. Search criteria are passed to Getrefs via the web interface, this returns a list of matching PMIDs from PubMed, these are then checked for duplicates, redundancy, etc. A second method is called in GetRefs.pm that is passed the PMIDs required and retrieves the text record for the desired references. This data is converted to a RGD XML format and passed to LoadRefs.pm which parses the reference data and loads it into the appropriate db tables.
PubFetch as a BioMOBY webservice
To provide generic access to PubFetch we intend to make the core functionality available as a webservice, following the BioMOBY service model. The two actions described above will be implemented as two classes of webservices, the first taking keywords and returning PubMed IDs (or other LitDb accession) , the second taking LitDb accessions and returning the text information in a simple, standardized XML format. We will endeavour to provide the data in existing formats (raw data from the LitDb, a BioPerl-compatible format, etc) in addition to a simple XML format that is not dependent on other codebases.
The fundamental actions required of PubFetch are as follows:
- Search LitDb for articles matching certain query criteria (eg. keywords, date, author, etc). This will most likely entail passing the search critieria to PubFetch and retrieving a set of accession numbers (eg. PubMed IDs, PMIDs) for matching references.
- Retrieve the text information from the LitDb corresponding to a supplied accession number (eg. bring me the PubMed entry for PMID 12345)
This is the procedure folliwed by the existing RGD modules. Search criteria are passed to Getrefs via the web interface, this returns a list of matching PMIDs from PubMed, these are then checked for duplicates, redundancy, etc. A second method is called in GetRefs.pm that is passed the PMIDs required and retrieves the text record for the desired references. This data is converted to a RGD XML format and passed to LoadRefs.pm which parses the reference data and loads it into the appropriate db tables.
PubFetch as a BioMOBY webservice
To provide generic access to PubFetch we intend to make the core functionality available as a webservice, following the BioMOBY service model. The two actions described above will be implemented as two classes of webservices, the first taking keywords and returning PubMed IDs (or other LitDb accession) , the second taking LitDb accessions and returning the text information in a simple, standardized XML format. We will endeavour to provide the data in existing formats (raw data from the LitDb, a BioPerl-compatible format, etc) in addition to a simple XML format that is not dependent on other codebases.