About Us & FAQ for Quertle® - the semantic biomedical literature search engine covering PubMed, full-text, news, and more.

Find relevant results in context,
not just long lists of documents

About Us and FAQ

General information about Quertle

Queries

Results

Filters

MyQuertle

Miscellaneous Issues

General information about Quertle

How is Quertle different?
More than simple keyword searching: Quertle goes beyond simple term matching to identify the most salient information in the literature. Using a combination of linguistic methods, Quertle finds facts defined within documents, creating its own database of about 300 million relationships, and is able to report the ones that are relevant to your query. Quertle's approach is based on a thorough understanding of biology and chemistry and was built from the ground up to address the unique needs of this technical literature.

Power Terms™: Quertle is able to extend its extensive biological and chemical sciences underpinnings to the definition of "Power Terms" that represent a class of entities. For example, the Power Term called $Proteins represents all protein names, thus enabling unique queries such as "what $Proteins regulate cell cycle?". Try it!

Easy exploration: Quertle provides a set of useful filters directly on the results page to help you navigate and explore the results. The "Key Concepts" filter automatically lists key concepts found in the result set so you can quickly focus in on concepts of interest. When a Power Term has been included in the query, the "Key Concepts" filter presents members of the Power Term class to answer your question. For the above example, all proteins that are involved in the regulation of cell cycle will be presented.

What content does Quertle cover?
Quertle uses MEDLINE/PubMed^® as provided by the US National Library of Medicine (NLM) (see Terms) and full-text documents from BioMed Central and Open Access articles from PubMed Central. In addition, Quertle covers the NIH RePORTER database of grant applications and the National Library of Medicine's TOXLINE database of biochemical, pharmacological, physiological, and toxicological effects of drugs and other chemicals. Quertle also searches News (as reported by FierceMarkets Life Sciences and Health Care) so that you can find late-breaking information without waiting for full publication) and scientific whitepapers and research posters submitted to Quertle (contact us about submitting yours). Additional full-text document sources are coming. Let us know what you think we should add next.

How does Quertle Work?
Underlying Quertle's ability to find relevant relationships are:

An extensive ontology - Consisting of dictionaries, thesauri, hierarchical and non-hierarchical relationships, these manually-curated databases are based upon information extracted from a wide variety of sources. The ontology also contains verbs (e.g., so we know "activate" and "induce" are related) and the collections of related entities (Power Terms).
Entity identification engine - Using the ontology, the entity identification engine recognizes and tags known objects. Recognition of gene and protein names is validated by the content of the surrounding text.
A versatile linguistic engine - This engine uses biomedical-specific natural language processing (NLP) for full-sentence parsing. The processing uses a syntactic parser to find possible sentence structures followed by conversion to a semantic tree. The primary result of that process is the identification of each subject-verb-object triplet, with each triplet normalized to active voice (for instance, "apoptosis is regulated by p53" -> "p53 regulates apoptosis").
A database of relationship triplets - Each subject-verb-object triplet identified by the linguistic engine is stored in a meta database. Quertle's database contains over 300,000,000 of these triplets.
A collection of very small elves that live inside the quertle.info server - Well, maybe not really, but functionally some elf-like software identifies the possible triplet structure(s) in your query. For example, "p53 regulation" could mean "p53 regulates ___" or "___ regulates p53" (see Quertle Tips for some useful hints on how to make such searches more effective). Then, your query is normalized to active voice. Next, the elves compare the possible triplets from your query to the database of relationships. That comparison uses the ontology to match entities against any alternative or variant names as well as any children in the structured vocabulary.
Relevance engine - This component ranks the resulting documents by relevance to your query using linguistic comparative algorithms. For example, a document with multiple matching relationships will rank higher than a document with only one relationship.
Key concept identification engine - A set of linguistic statistical algorithms are applied to the phrases containing the most relevant matching relationships; this identifies the concepts associated with your search results.

How does Quertle Handle Full-text Documents?
For full-text documents, Quertle searches the full content, not just the title and abstract. This includes Material and Methods, Figure Legends, etc. But, we do NOT search the references - only the text written by the author - so that you get a much more relevant list of results.

Where does the Name Quertle Come From?
We are asked about this a lot! Quertle was meant to be a memorable name reminiscent of "query". No one named Myrtle was involved. But "article" is relevant/ What we didn't want was yet another PubMed variant. There are too many of those already and with Quertle being a completely different way of searching, we felt the site deserved a completely different name.

Who is behind Quertle?
Quertle has been created by biomedical scientists, chemists, and literature informatics experts, who have many decades of experience with research and finding relevant information to support that research. Leading the effort are Jeff Saffer and Vicki Burnett. Quertle is headquartered in Henderson, Nevada.

Jeff has been involved in biomedical informatics for more than two decades and has a special interest in helping people understand large volumes of data. Following his PhD from Yale, Jeff was a fellow at the National Cancer Institute and then an Associate Staff Scientist at The Jackson Laboratory. He then was Head of the Molecular Biosciences Department at the Pacific Northwest National Laboratory. Throughout his research, Jeff used informatics approaches to make the most of data. It was during his tenure at PNNL that he founded OmniViz, which focused on the visualization of biomedical data, including literature.

Summer at altitude

Vicki also has a long history of applying informatics and data analysis. She received her doctorate in molecular toxicology from the North Carolina Integrated Toxicology Program (Duke, UNC, NC State). Vicki did research at CIIT, the National Institute for Environmental Health Sciences, and the Pacific Northwest National Laboratory prior to joining the University of Arizona as Associate faculty at the Health Sciences Center. She then joined OmniViz and became a key contributor to the design of that software.
Playing at Fenway Park!

When did Quertle get Started?
Quertle went live May 18, 2009 with its beta version. The full version of Quertle launched exactly six months later on November 18, 2009.

Why the ads?
Political answer: To help you find knowledge, including products relevant to your work.
Practical answer: Without the modest proceeds, we couldn't provide this site for free.

Note that advertisements do not influence the results in any way, including what is found or relevance.

Queries

How should queries be written?
Searches on Quertle are best constructed in the form of a subject-verb-object relationship, or any part(s) of such a relationship. For example, you could write "aspirin treats headache" to find all documents about that subject. You can also use "what" for the subject or object as in "what treats headaches?" (to find documents on anything treating headaches) or "aspirin treats what?" (to find documents on what aspirin treats). Or, you can simply enter one or more terms. See Help for details.

Are queries case-sensitive?
Yes and no. For most terms, case does not matter. Some terms, however, have very different meanings when used in a particular case. For example, consider "NO" (nitric oxide) and "no" (negative), or "AIDS" (disease) and "aids" (helps). In these cases - pun intended - it is a good idea to use proper capitalization. And, for the record, font size doesn't matter.

Can I enter a query with Boolean logic (AND, OR, or NOT)?
No. Since Quertle attempts to interpret your query as a subject-verb-object relationship, you should not include Boolean operators. It is better to add additional terms (AND) using the Also Containing filter.

Can I look for a specific phrase using double quotes?
No. Quertle "conceptualizes" your query to give the most relevant, and generally increased numbers of results. Quertle takes input such as "pinocytosis inhibition" and matches that to relationships, including "fluid-phase endocytosis was inhibited by" and so on. Thus, forcing a search for specific phrases is not supported. Quertle also "knows" about most things biological and chemical and will automatically recognize phrasal entities, such as "muscle contraction". If Quertle doesn't seem to understand something, please let us know.

What Power Terms can I use?
Power Terms are query terms used to represent a class of entities, such as $Diseases (representing all diseases), not the generic term "disease". The most commonly used Power Terms can be found in the Power Terms pop-up window. This can be accessed by clicking the link below the Search box. You can also view the full list of Power Terms. If there is a Power Term you think should be included, please let us know.

Can I create my own Power Term?
No. You cannot simply add a $ at the beginning of a query term to make it a Power Term, since Quertle has to assign the members of each Power Term in the ontology. If you want your term included, let us know.

What does the $ mean?
The $ signifies that the search will be for the members of that Power Term class BUT NOT for the term itself. For example, the word "disease" is very common in the literature and it is not always helpful to search for that. Instead, if you want to find actual diseases - but not "disease", "syndrome", etc. - then the Power Term $Disease is what you would use. Automatic Power Terms (such as "neurotransmitter") do not have the $, signifying that the term, its synonyms, and members of the class will all be found.

Can the Power Terms be typed into the query or must they be picked from the pop-up?
Yes. The pop-up list is a convenient way to enter the Power Terms, but you can also enter a Power Term by typing it directly in the Search box. But be sure to check the full list of Power Terms periodically, as Quertle will be adding new Power Terms all the time.

Are MeSH terms used?
No and yes. Relationship-based searches are looking at text written by the author for assertions that tie your search terms together. MeSH terms are not written by the author, nor do they necessarily imply a relationship. For example, an article on adverse effects of drugs that states "doxorubicin causes congestive heart failure" and "dofetilide causes long QT", does not imply doxorubicin causes long QT even though both would be MeSH terms. Thus, for results found on the Relationships tab, the search does not use MeSH.

Having said that, we note that MeSH terms can be extremely useful. So, once the documents are found to contain author-asserted relationships that match your search terms, drilling down using the Also Containing filter does use MeSH.

MeSH terms are also used for the keyword-based searches. These results, on the Keyword Results tab, are not relationship-based and look in all the informative sections of the document (text as well as the MeSH, chemical, and gene lists provided by NLM).

How do I search for an author?
Stand up and look around the lecture hall. OK, a better answer: unlike some other sites, you should not enter the author(s) of interest in the main Search Box. Please type in the author(s) of interest in the Author Search box. As you type in an author's name, a list shows some possible matches. As you type more, the list will update accordingly. You do not have to actually pick from the suggestion list if you prefer to type the entire name. You can search for multiple authors by entering more names in the Author Search box, each separated by a comma. If more than one author is entered, the results must contain all of the names.

What if I don't see the author I am looking for in the suggestion list?
Keep typing. The list cannot show all possible matches (e.g., if you are looking for "Smith") and shows the more prolific authors that match what you have typed so far. As you type further, you should see who you're looking for. If you don't, then either that person used a pseudonym or we lost them. In the latter case, please let us know.

How do I search for a specific journal?
To limit your query results to those from a specific journal, enter the journal name in the Journal Search box. As you type in a journal name, a list shows some possible matches. As you type more, the list will update accordingly. You do not have to actually pick from the suggestion list if you prefer to type the entire name. You can search for multiple journals by entering more names in the Journal Search box, each separated by a comma. When entering multiple journals, the results will be for any of the entered publications.

What if I want to search by author or journal without any other terms?
No problem. Just enter the author(s) and/or the journal(s) and leave the main Search box empty. There will, however, not be any relationship type results listed in the "Key Concepts" filter area, but all documents by that author will show up. You can further filter to a topic of interest simply by adding a term in the "Also containing" field found on the results page.

How do I limit the dates being searched or apply other filters?
The date, publication type, and term-based filters for Quertle are found directly on the results page. Do your query first and then limit the results as desired afterwards.

Results

What's the difference between Focused Results and Broader Results?
Focused Results are documents that contain relationships tying your search serach together in a meaningful way (conceptual facts extracted by linguistic methods). Relationships are more than just having the terms found in the same document and are based on the context and implication of the text. The result is a set of documents that are highly focused on your query.

Broader Results are documents found by doing a keyword search for your query terms - and their synonyms - regardless of whether the words are used within the same context, or even within the same section of the document.

Why are there fewer Focused Results than Broader Results?
In most cases you will find fewer results on the Focused Results than Broader Results. When searching for multiple terms, the Focused Results show documents that use the multiple terms together in a meaningful way, whereas the keyword search will find more documents because the terms do not have to be together. Even when your search is a single term, the Focused Results results only contain documents where the term is used in a recognizable relationship.

What is the highlighting?
The terms and phrases highlighted in yellow are your query term(s). If you have added an "Also containing" filter or have clicked on a Key Concept, those terms will be in bold. If you prefer not to have the highlighting shown, click "Turn Highlighting Off" at the top of the results. To turn it back on, click "Turn Highlighting On". If the matching term occurs in the MeSH terms, the Chemical list, or in another part of the body of the document, that match will be presented at the bottom of the result listing.

Why are some terms italicized?
Quertle recognizes abbreviations on a document-by-document basis. When a relationship contains a recognized abbreviation, that abbreviation is italicized.

How are the results ordered?
Quertle initially orders the results list according to what is most relevant to your search.

Can I reorder by date?
Yes. Simply click on "Sort by Date" at the top of the results list. The results will now sort by date, most recent first. To go back to relevance sorting, just click on "Sort by Relevance".

What does the date "Epub" mean?
Many publishers submit accepted articles to PubMed prior to their actual publication. These articles have a publication date sometime in the future. Quertle shows all such future dates as "Epub" (Electronic publication ahead of print) so you don't run off to the library and wait for several months for the article to appear.

Why can't I filter by more than one Key Concept at a time?
Currently, Quertle does not support selecting more than one Key Concept for filtering at a time. Here is why: Quertle is actually searching for subject-verb-object relationships (triplets), such as "A causes B". This is how we focus our results on what is most relevant to your search. More often than not, the relationship triplet does not contain multiple subjects (more than one "A") or multiple objects (more than one "B"). Thus, selecting more than one Key Concept (A's, B's, or modifiers of A or B) will often leave no results. If you believe a second Key Concept would be relevant in your filtering, simply enter that concept as an Also Containing filter, which allows unlimited, independent terms.

Can I save or export my list of documents?
Yes. You can export selected results or all of the results (up to 1000) directly to your bibliographic manager software or to a file. The Results pages are also Zotero-compliant. See Help for guidance on using the export feature.

Filters

What types of filters are available?

Also Containing: You can type in additional words to be searched for in the current results set by typing into the "Also Containing" text box, then click the >> button (or by hitting Enter). This will filter documents to those that contain the additional terms anywhere within the informative text - title, abstract, body (for full-text), MeSH terms, or Chemical list. The "Also Containing" filter always looks for the term you enter, all of its inflected forms (such as plurals), all of its synonyms, and all of its "children" in the ontology (for example, "rodent" will find "mice", "rats", etc.).
Published Within: Documents can be filtered by date to show only those published within defined time intervals, such as the previous 30 days. Let us know what other date ranges would be useful.
Publication Type: Documents can be filtered to show specific types of publications. Simply click on the publication type of interest. Note that clicking more than one publication type will filter the results to ANY of the selected types. To undo your choice(s), simply delete the Publication Type from the Applied Filters or click the individual entry in the Publication Type filter. Let us know what other publication types you would like to be able to filter by.
Key Concepts: One of the most useful aspects of the filter set is to limit documents to those relevant to a concept of interest. The "Key Concepts" filter section contains terms Quertle automatically identifies as key concepts in the initial results set. And when you have used a Power Term, this section presents members of the Power Terms group that are part of the identified relationships. Click on any term in the "Key Concepts" section to show only those documents containing the specific results of interest. To undo the filtering, just delete the term in the Applied Filters section.

How do I use the Applied Filters?
When you apply a filter, a "breadcrumb" is left in the Applied Filters. You can eliminate any (not just the last) filter by clicking the corresponding or by clicking the entry again in the filter section. You can also go back to a prior set of results by clicking on a breadcrumb link, which removes all filters below it. To remove all filters, click the following the Applied Filters label.

Can I apply more than one "Key Concept" filter?
No, but you can remove the current filter and choose another one simply by clicking on the next to the term in the breadcrumb trail. Or, just click on a different term in the "Key Concepts" list and the filter will change.

I know a certain object should be on the "Key Concepts" list, but it isn't. Why?
The top concepts (or members of a Power Term class) are calculated from the most relevant documents. The term you are looking for is likely far down the list of results and may not have been included in the relevant set. You may want to use a different query.

MyQuertle

What is MyQuertle?
A MyQuertle account allows you to save and easily re-execute searches. You can also have automatic alerts sent to you each week that will show any new documents that are found by your saved search. Your MyQuertle account also allows you to set your preference for number of results to show on each page and to choose the institution - enabling you to access results documents through your library's subscriptions.

What happened to the Key Concept I saved with my search?
Key Concepts are the most relevant concepts associated with the relationships found by your search. As new documents are added to Quertle, an old Key Concept may become pushed down in relevance and hence no longer "key". This should be a rare occurrence, but with the rapid changes in science it is possible. If you want to limit your search results to those contained the "expired" Key Concept, simply apply that term in the Also Containing filter.

Why don't I see a My Library link with each result?
You must be logged in to MyQuertle and have selected your institution from the drop-down list of organizations to see the My Library link. If your organization is not in the drop-down list (i.e., you chose "Other" and entered your organization name), we are working to connect your institution's subscriptions to Quertle results. You can help by asking your librarian to submit a request. It's quick and free.

How do I get Alerts for my saved searches?
On your MyQuertle Saved Searches page, simply check the checkbox for the search(es) you want Alerts for.

Why didn't I get an Alert this Week?
An Alert is only sent if there is a newly added document that meets your saved search criteria.

Why is there an old paper in my Alert?
You may occasionally see an older document in your MyQuertle Alert. This can happen when that document was recently added to the databases used by Quertle. For example, if a new journal is added to PubMed and back issues are newly indexed, you may see one of those articles if it matches your search criteria.

Why am I asked to log in when I already did that?
If you choose for Quertle not to remember you when you logged in (for example, when you are on a shared computer), your session may time out. This is to prevent unauthorized access to your MyQuertle searches and settings. Simply log in again and, if you are not on a shared computer, consider having Quertle remember you.

Miscellaneous Issues

Why don't some links and actions work in my browser?
Many controls on the Quertle site - including links to the Power Terms and View Examples and the Clear All button - require javascript to be enabled. To enjoy the full functionality of the Quertle site, you should allow javascript to run in your browser.

Can I add Quertle searching to my own web page?
Yes. You can add the Quertle gadget.

Quertle® is a Registered Trademark of Quertle, LLC.