Over the last decade we have succeeded in making GenomeQuest the industry standard for biological sequence searching in IP. We did this through the combination of specialized IP search algorithms and what has become the world’s largest IP sequence database (let alone the largest sequence database on earth) through a combination of automation and manual curation of patents from global patent authorities.

Not so long ago we launched LifeQuest, a new product that allows you to search the full text of all life sciences related applications and patents. We created it in close collaboration with our many existing customers, and we really tried to listen to them. They honestly believe that using LifeQuest will make you more productive and allow you to do things that you couldn’t do before. Here are the five things that they think you should know about:

  1. Browse and search full text. The records in GQ-Pat contain the basic bibliographic information, but LifeQuest takes this one step further by making the complete text and the PDF of the document available as well. To make sure that you get the most out of this we added fully featured query and highlighting capabilities using life science ontologies to help you find better results.
  2. Combine sequence and full text searches. If you move search results from GenomeQuest over into LifeQuest, it also transfers the sequence alignments. This feature, for which a lot of customers asked us, makes it possible to combine multiple sequence and full text searches in LifeQuest without losing sight of the alignments themselves – something you’ve been unable to do in GenomeQuest till now.
  3. Updated USPTO PAIR information. A PAIR record details the interaction between a patent applicant and the USPTO. People use it to find out if a patent is still active, had its term extended, is open for prosecution, or had its claims limited. The USPTO makes access to this data difficult by hiding it behind CAPTCHAs and query forms. In LifeQuest, up-to-date USPTO PAIR information is readily available for all US documents. You can use this to your advantage and get work done more quickly.
  4. Monitoring and alerting. LifeQuest makes it really easy to monitor large lists of documents. It will tell you right away when things are granted, when a Kind Code changes, or when new members are added to a patent family. In addition you can automatically repeat a previous search at a regular interval and get an email when something new has been found.
  5. Search result annotation. Once GenomeQuest results are inside LifeQuest they can be annotated using color coding and star ratings. When combined with the fully customizable table display and the export capabilities to Excel, it will allow you to quickly review a large list of documents and share it with others in the organization.

So if you’re already a GenomeQuest user, or just someone who is interested in doing full text searches for life science patents and applications, you can sign up to demo LifeQuest today.  Sign up for a free trial.

What to Look for in US public PAIR

us-patent-office-bldgLike most people that work with patents, I have always understood that USPTO’s Patent Application Information Retrieval (public PAIR) is the USPTO’s way of sharing information on where a patent application is in its lifecycle. It is a critically important resource because it provides the most up-to-date US patent information. Still, I was a little overwhelmed when we began adding all of that information to our LifeQuest product a couple of weeks ago. It was clear that I had some serious catching up to do.

Did you know that prior to 2002, the only way to get up-to-date information was either by going to the USPTO in person, or by ordering a copy of the file history through snail mail? Since there was no way to know in advance how big a file would be, and because they charged by the page, this could be an expensive and time-consuming procedure.

Today, all this information can be accessed on the USPTO web site, but accessing it can still be a bit of a hassle. To prevent people from scraping the information from the web pages, the good stuff is hidden behind many mouse clicks and a test to prove that you are really human. While this may work well to protect USPTO information, it kills productivity for us normal patent searchers, especially when we have many documents to lookup (which is most of the time!)

Now for the good news: GQ Life Sciences has obtained access to the same underlying data source that the USPTO uses to update their public PAIR portal, and we’ve added this continuously updated information to all US documents in LifeQuest.

The USPTO organizes PAIR data in a tabbed interface (we’ve done the same in LifeQuest). Wondering what you can dig up when performing your search? Here are five key things to look for:

  1. The Application Number

If the document you’re looking at has been granted then you can use this number to retrieve the original application.

Where to find it: LifeQuest Bibliographic Data Tab

  1. Pre Grant applications that have been abandoned.

This is the first and most reliable place to see if an application has been abandoned by the people that submitted it.

Where to find it: LifeQuest Bibliographic Data Tab

  1. Complete communications history between the examiner and the applicant.

Here you can see interesting things like how thoroughly the application was examined, or if the claims have been limited in some way.

Where to find it: LifeQuest Transaction History Tab

  1. Examination delays and extensions that have added time to the term of the patent.

The delay is added to the standard term of the patent, which normally comes down to 20 years starting from the earliest priority date.

Where to find it: LifeQuest Patent Term Adjustments and Extensions Tab

  1. Basic family members that are open for prosecution.

US PAIR lists any US applications that came before or after the current application that also claim benefit from/to it.

If the list has a pending application in it, the family is open for additional prosecution, meaning that new applications that claim benefit to an earlier priority date can still be filed (the family can still be extended using the earlier priority date).

You can also see additional granted patents and PCT applications, a clear indication of value for the application or patent you’re looking at.

Where to find it: LifeQuest Continuity Data Tab

Public PAIR is available for all granted US patents and published US applications.  It allows anyone to look at the details surrounding the prosecution of an application and the interaction between the applicants and the USPTO.

By studying this data, it is possible to determine if a patent is still active, had its term extended, was examined thoroughly, is still open for prosecution, or had its claims limited. Connecting this valuable information with full-text search results is just one of the ways we aim to make patent research easier and more productive.

How do you like to use US Public PAIR data in your research?  Share your thoughts in the comments below.

Searching through USPTO Public PAIR data is only one of LifeQuest’s many capabilities.  Sign up for a free trial today and search for Public PAIR data and more patent information with ease.

Earlier this month, GenomeWeb featured an article entitled, “GenomeQuest Rebrands as GQ Life Sciences, Refocuses on Patent Search Market”.  We’re pleased to have our company’s growth recognized by one of the leading independent science news publications.

Uduak Thomas, who wrote the article, did a great job chronicling our company’s timeline from its early days through the progression of our products that have grown from a database of patented gene sequences, to our foray into analyzing next-generation sequencing (NGS) data, to our most recent product, LifeQuest, which is one of our most ambitious projects yet.

As our portfolio of life science patent search products continues to expand, it’s inspiring to see customers accomplish exciting, even unexpected things that make significant contributions towards helping solve huge, global problems. ADM, one of our customers mentioned in the article, uses our databases to explore patents to look for ways to convert agricultural raw materials into other products, including food for humans, feed for animals, and bioenergy. They’re even using our data to research ways to design probiotic feed inoculants to replace antibiotics for farm animals.

As we head into the new year, our team is excited about the opportunities ahead for our customers. Our development team is working hard to add additional public and proprietary data sources to LifeQuest, starting with peer-reviewed scientific literature. We continue to receive great feedback about the user interface in LifeQuest, and we have some great ideas to make it even better. We’re certain that other exciting new discoveries will be found even faster as researchers discover the power of combining sequence data with full text search results in LifeQuest.

Download the article.

lifequest-logo-512562-editedLike any molecular biologist that has worked in pharma research, I have searched through and read a lot of scientific literature. I like to think that I’ve gotten pretty good at it. I’m always surprised though, when I run into colleagues who don’t spend much time searching patents on a regular basis. I understand that the patent world can seem daunting and confusing, and even knowing where to start is difficult, but there are pretty strong arguments for including patents the next time you research a topic.

1. Stop wasting your budget.

It has been estimated that up to 30% of all R&D expenditure is wasted on redeveloping existing inventions [1]. Most of these unnecessary costs can be avoided by searching existing knowledge on a topic first. While many researchers diligently go through scientific literature and books, they often forgot about patents. Patents are a large,  up to date source of information on applied science and technology, and should be included in all state-of-the-art searches.

2. Find relevant information not found anywhere else.

Patents contain a lot of information that is not published in scientific journals. The European Patent Office (EPO) claims that up to 80% of current technological knowledge can only be found in patent documents [1]. This is because overall it is easier to file a patent than to publish a peer-reviewed paper, and with patents there are no restrictions on the number of pages used to describe the experiments and results. Also, as a matter of policy, many companies do not disclose their R&D results in any other way than through patents.

3. Find this information sooner.

Being the first to patent something, the right of priority, gives people a strong incentive to file early and disclose all information in a great amount of detail. In many patent authorities, as soon as a patent application is filed it becomes available to the public after which it should be included in state-of-the-art patent searches.

4. Find high value information.

Filing a patent costs time and money, and companies generally do not do it unless they think their invention has value to their business. If it has value to them, then you should probably know about it as well.

5. Get free inventions.

Many patents are no longer valid. Not only do they expire after 20 years, at which point anyone can use the invention, many are also abandoned much earlier in the patent life cycle because fees are not paid on time or because they simply do not get granted. Around 85% of all patents are no longer in force or have never been in force [2]. These are free inventions for anyone’s  use.

6.Use granted inventions as well.

Even when a patent is in force it can still be useful to know about it. In some situations the invention may be used for experimental purposes. Also, a researcher might decide to consult an IP specialist in the company and change research direction, or license the invention from the patent owner. Of course, anything that is not explicitly mentioned in the patent claims is always free information.

7. See what the competition is doing.

Patent searches are the perfect way to gather business intelligence and monitor innovation strategies of other players in the field very early on. Use this information to your advantage and adjust your own R&D strategy or find potential collaborators this way.

8. Prepare for filing your own patent.

The only way to prove that an innovation is really new is to search all existing knowledge, including the patents. In fact, examiners at the patent office will always search existing patents before they try anything else.

9. Search the full text, not just the abstracts.

For commercial reasons, the full text of scientific articles is often locked behind a paywall. As a result, popular literature search tools will only let you search the abstracts, causing you to miss a lot of important information in the rest of the article. Patents are always available as full text, giving you the choice of searching only the abstracts or searching all text.

10. Searching patents is easy to do nowadays.

Gone are the days when patent searching required extensive training or the assistance of an IP specialist. With a web-based patent search tool like LifeQuest it is very easy to search an always up-to-date database of life science patents filed anywhere in the world. LifeQuest helps you construct better queries using suggestions of synonyms for your search terms that are pulled from life sciences ontologies like MeSH and Gene Ontology (GO). It also helps you manage your search results, so you can find the most relevant things quickly. There are no more excuses for not searching patents.


  1. As estimated by the EPO here: http://ec.europa.eu/invest-in-research/pdf/download_en/patents_for_researchers.pdf
  2. WIPO IP Statistics Data Center http://ipstats.wipo.int/ipstatv2/keyindex.htm


We are proud to announce that there are now over 300 million sequences in GQ-Pat, including 256 million nucleotide sequences and over 45 million protein sequences. And these protein sequences aren’t just automated translations of nuceotides like TrEMBL. All of these sequences are in fact found in patents and patent applications from patent authorities around the world.

To put this accomplishment in perspective, when the Human Genome Project formally began in 1990, there were fewer than 40,000 sequences in GenBank, before being transferred from Stanford to the newly created National Center for Biotechnology Information (NCBI).

As of the summer of 2015, according to the NCBI’s GenBank Statistics page, there are 185 million nucleotide sequences in GenBank/EMBL/DDBJ consortium, the world’s gold standard for sequence databases.* GenBank represents merely slightly more than half of GQ-Pat!


Not only does GQ-Pat have double the sequences of GenBank, these sequences help searchers in other ways as well:

  1. The sheer size of the database itself helps organizations save money through efficiency and the fact that important search results won’t be missed.
  2. Sequences in GQ-Pat are well annotated because all of them have been found in patents, making them more valuable to researchers. Patent information includes descriptions of a particular invention, including the way in which the invention is used, the inventors, the owners, biological information about the sequence, its function, and so on.
  3. Researchers using GQ-Pat can obtain results much sooner than those using public databases like GenBank because patents are typically filed before publications are drafted.

We’re so pleased that more and more researchers are turning to GQ-Pat to search sequences for a huge variety of life science related projects. Our clients point out that when it comes to researching or protecting their own intellectual property, the quality of the results are often only as good as the size of the database they come from. That’s why we’re dedicated to maintaining the world’s largest. Of course, we’re also adding rich annotations and making sure updates are added on a weekly basis.

If you’ve never tried it, and you’re interested in searching our 300 million sequence (and growing) database for yourself, there’s never been a better time to get in touch about a free trial.

* There are another 50 million protein sequences in Uniprot, the leading protein sequence database, although 98% of Uniprot is TrEMBL, which consists of 49 million unreviewed computer-generated protein translations of nucleotide sequences already in the nucleotide databases.

Integrated Full-Text and Sequence Search

Prior art searching in the life sciences is complicated. Tens of millions of patents and applications, dozens of file formats, and handfuls of search platforms force the professional patent searcher to jump through hoops to get answers.

You know GenomeQuest as a Leader in Intellectual Property Sequence Searching.

But we’re branching out to bring you an integrated keyword search platform that is designed for life science patent searchers like you. It’s a full-text search product that we’re calling LifeQuest.


LifeQuest has deep integration with life science ontologies, combined with the most modern search indices, fast navigation of results using keystrokes, set operations on search results, and tight integration with sequence search. It’s being launched in April, 2015.

Download our white paper or Free Trial to LifeQuest today.


Because GenomeQuest’s GQ-Pat is a document database rather than a family database, you might hit the same sequence more than once because it occurs in document A and document B both in the same family. That’s actually incredibly useful because it allows you to examine how sequences found in patents change from patent family member to family member.


What if you could collapse this down so that each unique sequence in a family was represented only once? That would unlock lots of use cases, for instance:

  • removing all redundancy and showing you the top hits to your query for each family, rather than by document
  • breaking down a sequence’s legal status, SEQ ID NO, or claim information as it moves through different family members
  • examining a non-redundant view of the unique projection of sequences across an entire family

This video explains GenomeQuest’s Unique Family Sequence (UFS) capability and how to maximize your use of it.



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Each year, pharmaceuticals, biotech organizations, academic institutions and law firms commit costly errors that happen due to poorly informed IP portfolio decisions. Relating to biological sequence search, here are nine serious mistakes we hate to see life science companies make.

1. Overlooking patent sequence data.

Serious sequence information search require specify and organized efforts, and searching Genbank is not enough. Genbank had 180 million sequences as of its December 2014 build, only 32 million of which are identified in their patent division. As a contrast, GenomeQuest’s GQ-Pat had over 280 million sequences, all found in patents, almost nine times larger.


2. Under-utilizing annotation information.

Ascertaining the legal or biological importance of the similarity between any two sequences requires a clean, curated database with organized annotation fields and content. Additional fields, such as bibliographic references, date of earliest publication, and date of sequence disclosure add analytical speed and precision when used with a rapid search result filtering function.

3. Forgetting the Dark Genome.

Public BLAST portals search only the most readily-accessible elements of the entire universe of genome data. The remaining information is sometimes referred to as the “dark genome.” Poorly annotated data in a readily accessible database may be considered part of the dark genome, in that is “hiding in plain sight.” Additional data with low search accessibility includes the information held in proprietary databases, desktop hard drives, graphic images and illustrations, and print document collections. Searching the “dark genome” requires access to proprietary data and full-time, multiple-media genome information searching and database curation procedures.

4. Taking too much time.

Taking too much time to do a patent-related search is a root cause of research project and intellectual property decision delays. Researchers might spend weeks scouring the internet for new data related to a query sequence, or developing lists of databases holding separate or overlapping sets of genomic information. Unintuitive search software user interfaces cause “learning curve” delays, and sequence search outsourcing can cause vendor transaction and project scheduling delays of weeks or months

5. Hoping for the best.

Moving forward with a research project without properly searching and evaluating sequences can prove to be costly in the long run. An incomplete evaluation of the data early in the research cycle can be costly once a completed project is found to have yielded unusable results.

6. Making decisions based on yesterday’s results.

Genome sequence information is extremely dynamic. In addition to the steady addition of recorded primary sequence data, scientific and patent information about both new and previously existing sequences also grows and changes on a daily basis. A sequence data query affecting important scientific research and business decisions might not yield the same answer one week from now. The more sequences involved in the decision, the greater the risk. Research groups and businesses without access to an automa

ted and continuous search-and-report system are particularly vulnerable.


7. Using the wrong algorithm.

Even the most experienced analyzers can make a mistake choosing the right algorithm for sequence search. For example, using BLAST for short sequences will miss many approximate hits. GenePAST is a better algorithm to use in many sequence search cases.

8. Too many gatekeepers.

Restricted access rights to proprietary databases, cumbersome search software user interfaces, and outdated business practices often prohibit direct utilization of sequence data search systems by the person asking the question, who must instead work through one or more gatekeepers. A well-defined project submission process can prevent intended queries from getting “lost in translation,” but when sequence searches are outsourced, queries are often composed broadly in order to prevent potentially relevant results from being excluded from the search report returned by the service. This results in an oversized report and a long manual search process for the sequence records of real interest. Gatekeeper delays also inhibit creative sequence data exploration, where hunches and hypotheses can be quickly formed and investigated using fast, iterative database queries.

9. Ignoring workflow issues.

Commercially licensed or in-house bioinformatics solutions often become very popular within organizations as researchers learn to use them to great advantage. But an effort to provide genome search capability to the user base that does not consider workflow issues can result in the installation of an isolated, standalone information “silo” with an unfamiliar interface. The standalone solution is itself likely to be underutilized, and also fails to take advantage of organizational knowledge built up around previously existing bioinformatics applications.


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Antibody Patent Searching Made Easy

Researchers often neglect to search antibody patents because it seems complex and due to the perception that there is nothing to be gained from it. Dangerous thinking!

Antibody searching, with the right tools, is in fact quite easy. And the gain is compelling: searching patents is the best way to learn about the competitive landscape because patents are published before scientific papers.


All antibodies have significant sequence homology to each other since they all have the Immunoglobulin (Ig) domain. The functional part of an antibody query, its uniqueness, comes from short (5-20 amino acid) loops in the Ig fold called Complementarity Determining Regions (CDRs). Determining the similarity between the CDRs of different antibodies is the key to proper antibody searching.

This short video shows how easy it is to do antibody similarity searching in GenomeQuest.



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