Our products at a glance
GoPubMed Pro - Semantic Federated Enterprise Search
GoGene - Elucidate Networks of Genes
GoPubMed PRO - Corporate Semantic Search
According to a recent study, life sciences professionals spend an average of 12.4 hours per week searching for information - not only on the Internet, but also in company repositories, their own computers and emails. GoPubMed PRO semantic search technologies can significantly reduce the number of hours spent from 12.4 to just 1. This is possible through knowledge-based classification - the platform of the successful GoPubMed. Additionally, GoPubMed PRO includes an Ontology Generation and editing platform that speeds up the modeling of new fields or domains.
Scroll down to learn about GoPubMed PRO's broad array of features and how they can impact your search.
Product matrix
Intelligent semantic search - save 90% and more of your valuable time
Semantic search stands for the next generation of search technologies beyond keywords. By using knowledge in the form of semantic networks - also known as ontologies - GoPubMed has two significant benefits: the completeness of results is guaranteed and ultra-fast filtering of relevant results becomes possible. For example, GoPubMed knows that "Aspirin" has 17 synonyms and includes all of them in the search. For the query "Aspirin inhibits," it can be seen at a glance that the "cyclooxegenase pathway" is the most mentioned. Traditional search technologies cannot deliver these results.
Semantic navigation
Query the system without typing keywords. By just clicking on - multiple - ontology terms, the platform will expand the query using synonyms and children of this concept. This is true semantic search unseen in other systems available on the market.
Advanced semantic statistics
GoPubMed PRO's Advanced Semantic Statistics offers an efficient alternative for gaining an overview of biomedical literature. A bibliometric analysis platform provides various statistics on biomedical literature by taking into account all data: authors, journals, locations and institutions, lists of author networks and geographic information, as well as the development of a topic over time. Users obtain comprehensive information that allows them to quickly gain new insights.
Advanced search features
The system also allows for the design of advanced queries. The key is that all possible categories, like authors, affiliations etc., are based on background knowledge. A semantic auto-completion box shows the most likely concepts for a certain context. This simple but powerful feature speeds up query design while providing insights.
Integrated semantic community platform
Connect with professionals that share similar interests or research activities. The integrated semantic mash-up identifies collaborating people and clusters of persons on the internet or within your organization.
Search your own sources
Search selected internet sites, your desktop or your organization's intranet, databases and Microsoft SharePoint. GoPubMed PRO works with most file formats and APIs to databases. Internal highlighting is available for many PDF formats so that insights can be identified at a glance. Conduct semantic searches with "concept + synonyms + children". GoPubMed PRO fully guarantees the completeness and transparency of the search results through linking meta data with ontologies and content.
Use and edit your own ontologies
Customize your own ontology, your own "table of contents". Easily include other ontologies with more detailed information, for example, on diseases. The system was developed in close collaboration with our customers and was designed with the goal of keeping it as simple as possible, but not simplistic. The software is designed for domain experts with little or no knowledge in ontology design and knowledge engineering. The system supports OWL and OBO formats.
Semi automated ontology generation support
The Ontology Generation platform offers a fast approach to creating your own ontologies. Using a knowledge base developed over a two-month period by a trained domain expert, the ontology comprises approximately 80,000 synonyms and is currently used by www.Go3R.org, a search engine for alternatives to animal testing.
The exclusive automated term-generation tool allows: querying GoPubMed and extracting and ranking terms, as well as their abbreviations; saving and loading terms from clipboard; filtering terms with regular expressions; finding likely definitions for terms by querying Yahoo and MSN; and adding terms to the ontology.
Multilingual semantic support
The software can handle ontologies represented in multiple languages. The text mining will still find relevant texts (in other languages) with semantic quality. This means that navigation and search can be carried out in the user's mother tongue, but non-native texts can be retrieved, too. The advantage of this is the small amount of returned texts, which afterwards can be translated at a reasonable cost.
Integrated folksonomy
With GoPubMed PRO users can easily curate text-mined categories. An advanced semantic curator tool is integrated in the platform to quickly improve the text-mined data. This feature allows the system to learn over time, and the quality of text mining often attains 95-100% accuracy.
Improved Text Mining
GoPubMed PRO integrates the latest algorithms that were applied in the BioCreative competition. Additionally, the new quality can be evaluated in GoGene, a new platform for the elucidation gene, protein and diseases interactions.
Discover information
The Discovery feature allows users to find concepts bridging two different unconnected concepts. This unparalleled feature which becomes possible through semantics allows you true knowledge discovery!
Data security and personalized access (coming soon)
With this new feature, GoPubMed PRO will provide an elaborate user rights management system that not only addresses data viewing, but also the access rights to parts of the ontology. For example, person A can view the tree "Biological Process" up to depth level 3 only while person B - having more rights - can see all ontology levels. The system allows the differentiation of read/write and also supports groups.
Personalized semantic robots (coming soon)
The automated semantic alert functionalities unique to GoPubMed PRO allow users to customize the system to obtain information on the latest findings that are semantically classified to the ontology. Users can include the categories WHO does WHAT, WHERE and WHEN and receive updates in an email-like manner.
Integrated semantic blogging (coming soon)
The Transinsight Semantic Wiki allows collaborative blogging with an ontology in the background. The system analyzes the current writing context and, via a semantic auto completion method, suggests the concept(s) - not only terms or words - to enter. The web-based system enables the generation and editing of large documents online and text mining is done on the fly!
System Requirements
- Database Server:
- 2 CPU cores at 2 GHz
- 16 GB RAM
- access to 300 GB of fast storage for the database
- MySql 5.x database
- Application Server:
- 4 CPU cores 2,5ghz
- 16 GB RAM
- 50 GB HDD for the application
- Tomcat 5.5.x Webserver, Java Runtime 1.5.
- Allows to search for genes in many ways
- Offers semantic search for genes
- Scans all the literature in PubMed for genes and gene-related functions
- Shows information about each gene at a glance
- Brings it all together
Allows to search for genes in many ways
The GoGene interface offers many possibilities to search for genes. Put your query as you would normally do in GoPubMed to get all genes discussed in these articles. Or search for genes by names or gene EntrezGene IDs directly. You can also blast an amino acid sequence to retrieve genes with similar protein sequence.
Offers semantic search for genes
All genes are associated automatically to your background knowledge, which lets you search and filter your results in a semantic way just like in GoPubMed. For example, after selecting the concept apoptosis, only genes related to programmed cell death or its sub-concepts are listed.
Scans all the literature in PubMed for genes and gene-related functions, processes, mutations, and diseases
Using the Gene Ontology and Medical Subject Headings as background knowledge, we associate genes to biological process, molecular functions and diseases and mutations. All associations are linked to the literature for further reading and verification.
Shows information about each gene at a glance
See all known information about a gene at a glance with links to literature, EntrezGene and UniProt. Such comprehensive overview is nowhere else available on the web.
Brings it all together
Bringing it all together, known information about genes from gene databases (e.g. EntrezGene) and information from the vast amount of literature, GoGene is the most comprehensive resource for genes available today.
GoPubMed - Knowledge-Based Semantic Search
Searching is now sorted - Save up to 90% of your time
With sorted search results the user is finally in the driver's seat. We don't rank results - the user does with easy navigation! Consider the search for Aspirin, for example. Other search engines yield more than 40,000 results for this term; by using GoPubMed's subtle mechanism for refining searches these 40,000 can be reduced to the 9 relevant to, say, coronary thrombosis. Finding these 9 articles with traditional technology takes several hours and the searcher has to have enormous knowledge in the field of coronary thrombosis. With GoPubMed even untrained students find these relevant articles within 3 seconds. If you don't believe it, try it online at www.gopubmed.com. It's free!
Answer Questions
GoPubMed can help answer questions significantly faster, with more relevant results and much more elegantly. Consider the following examples:
- Which molecular pathways are inhibited by aspirin?
- What is Richard Axel from Columbia University working on?
- Which cellular component is the protein Rab5 associated with?
A search for "aspirin inhibits", "Richard Axel Columbia" or "rab5" on a classical search engine will return large numbers of unstructured results which do not answer the user's original question. A classical search engine has no background knowledge on molecular processes, functions, and cellular components.
GoPubMed uses such background knowledge on biological pathways, molecular functions, and cellular components, to name a few. The machine indexes search results using background knowledge and thus allow users to explore a large body of results in a structured manner.
With such background knowledge, the machines can actually answer questions!
- GoPubMed discovers that the most frequently mentioned pathway for "aspirin inhibits" is the cyclooxygenase pathway.
- GoPubMed discovers that the most frequently mentioned topic for "Richard Axel Columbia" is olfactory receptor activity (for this work he obtained a Nobel Prize in 2004).
- GoPubMed discovers that the most frequently mentioned cellular component for "rab5" is the endosome.
Another example shows how semantic search can help to safe life. Consider the question:
- What was known about CD28 in 2002
A key problem in search is that important documents are often difficult to find and might be missed entirely. For example, what was known about the drug target CD28 before clinical trials were run in 2006 with near fatalities? A search for cd28 in GoPubMed returns several thousand documents. GoPubMed even increases this number by offering to include synonyms of the gene such as TP44 in the search. But here comes the power of the engine: GoPubMed offers its relevant knowledge in an intelligent table of contents to drill down into the results. A click on suggested terms such as signal transduction, autoimmunity reduces the results to only a handful including a paper from 2002 warning: "This new perspective on CD28 function suggests that caution should be taken in the development of immunotherapies".
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