WO2008030111A2

WO2008030111A2 - Method of searching one or more databases

Info

Publication number: WO2008030111A2
Application number: PCT/NZ2007/000248
Authority: WO
Inventors: Matthias Thomas Frei
Original assignee: CARTESIAN GRIDSPEED Ltd
Current assignee: CARTESIAN GRIDSPEED Ltd
Priority date: 2006-09-06
Filing date: 2007-09-06
Publication date: 2008-03-13
Anticipated expiration: 2009-03-06
Also published as: WO2008030111A3

Abstract

The invention comprises a method of searching one or more subject genetic sequences maintained in at least one database. The method comprises receiving a user identifier from a user; checking the received user identifier against a plurality of stored user identifiers; checking an authorisation record of the user identifier; on detecting a match between the received user identifier and one of the stored user identifiers, receiving a query genetic sequence; searching the or at least one of the subject genetic sequences in the database(s) for one or more sub-sequences of the query genetic sequence; determining a search result based at least partly on the results of searching the database(s) for the one or more sub-sequences; returning the search result to the user; and debiting the user for the search result.

Description

METHOD OF SEARCHINGONE ORMORE DATABASES

FIELD OF INVENTION

The present invention, relates to a method of searching one or more databases. More particularly but not exclusively it relates to methods for providing search services to authorised users. The databases typically consist of collections of data on genomes and genetic sequences, whether DNA, RNA, or protein.

BACKGROUND TO THE INVENTION

Patent specification WO 2005/124596 describes a data collection cataloguing method. The patent also describes a catalogued database.

It is an object of the present invention to provide a method of searching a database such as that described in the above patent specification, or to at least provide the public with a useful choice.

SUMMARY OF THE INVENTION

The term "comprising" as used in this specification and claims means "consisting at least in part of. That is to say, when interpreting statements in this specification which include "comprising", features, other than those prefaced by this term in each statement, can also be present. Related terms such as "comprise" and "comprised" are to be interpreted in a similar manner.

This invention may also be said broadly to consist in the parts, elements and features referred to or indicated in the specification of the application, individually or collectively, and any or all combinations of any two or more of said parts, elements or features, and where specific integers are mentioned herein which have known equivalents in the art to which this invention relates, such known equivalents are deemed to be incorporated herein as if individually set forth.

BRIEF DESCRIPTION OF THE FIGURES

Preferred forms of the method of searching one or more databases will now be described with reference to the accompanying figures in which:

Figure 1 shows a preferred form system in which the method operates. DETAILED DESCRIPTION

Figure 1 illustrates one preferred form system 100 suitable for implementation of the method described in more detail below. A principal component of the system 100 is a search engine or portal 105. Search engine 105 accepts requests from authorised users for example HO_{1 N} to search databases 115_{t M}.

Users 110 each operate a computing device on which is installed client software. The client software includes a software library that can be integrated into other software applications. Alternatively the client software is a stand alone program with a user interface or web page content that runs inside an internet browser application.

A user operating the computing device first sends a user identifier over a data network to the search engine 105. The search engine 105 has access to an authorisation database 120. The authorisation database 120 contains a plurality of stored user identifiers and a related authorisation record. Each of the stored user identifiers represents a user that, based on a user authorisation record is authorised to request searches of the search engine 105.

To use the search services described below, a user installs client software or accesses a webpage related to search engine 105 on the user computing device. The user must licence the software from an authorised supplier and provide personal details to the search engine 105. The search engine stores the user details in the authorisation database and assigns a user identifier to the user. The user must also pay an access fee at the time of registration.

Following registration the user sends search requests to the search engine 105. The search requests typically comprise a query genetic sequence. The search pattern sequences in one form represent fragments of genomes or whole genomes, gene data, nucleotide sequences or proteins.

To conduct a search the user transmits a user identifier for example a user name and password to die search engine. The search engine then checks die authorisation database 120. If there is a match between the received user identifier and a stored user identifier in the authorisation database, and the user identifier has a valid authorisation record then die search engine elicits from the user a search request. The user then transmits the search request in the form of a search pattern sequence to the search engine. As described in WO 2005/124596, the subject genetic sequence could include a nucleotide sequence. This nucleotide sequence in one search technique is divided into several consecutive sub-sequences of a length defined by the user. One example given is

"ATCGTCGTTCAGCATACCGT". This sequence is divided into four sub-sequences each of five characters in length where the user has requested divisions of 5.

The search engine 105 is interfaced to one or more databases 115j _M Databases 115 are available to the search engine 105. The databases include arbitrary collections of data on genomes. The arbitrary collections include publicly available data as well as privately collected data and proprietary data. Included in these databases are databases on known genes of humans, animals, other creatures and plants as well as other genetic sequences of known or unknown function. The databases contain one or more subject genetic sequences

In one search technique a query genetic sequence is broken into different sub-sequences. The search engine 105 searches databases 115_1---M for one or more of these sub-sequences of the search pattern sequence. Patent specification WO 2005/124596 describes how the databases are catalogued using an index array and a location array to assist with searching.

The search engine 105 determines a search result based at least partly on the results of searching the or at least one of the subject genetic sequences in databases 115_{} M} for one or more of the sub-sequences. Where for example each sub-sequence provided to the search engine is found in a consecutive sequence stored in one of the databases, the result of the search will be that sequence. Where some but not all of the sub-sequences are found in the databases, search engine 105 determines the success or otherwise of the search and provides the search result back to the user.

The search results are returned to users or user HO_{1 N}. With each search request supplied by a user, a usage fee is due. The user is required to pay up front for any number of searches. After the search result is returned to the user, the user is debited a fee for the search result. The authorisation database 120, or an associated accounting component, keeps a usage account for each user to track paid fees against performed searches. If the number of prepaid searches falls below a specific threshold, the user is reminded that the user is required to top up the usage fee account by a payment. As described above, subject genetic sequences ate maintained in databases HS_{1 M}. It is envisaged that mote than one subject genetic sequence be maintained in each database. Each subject genetic sequence is maintained as a separate record. Each record includes at least two data fields. These data fields include a sequence identifier and the actual sequence data.

Many sequence data records have additional annotation fields. These annotation fields include details of submitter, function and source species. These additional annotation fields are associated with individual subject genetic sequences by storing the annotation fields in the same data record as the subject genetic sequences. Alternatively, the annotation fields are stored in a record that is linked or cross-referenced to the data record containing the genetic sequence.

It is usual for a user to keep a private set of annotations. This private set of annotations includes the user's personal reassessment of the function, what evidence would support that special function annotation, and what subsequent work is being done with that sequence. In one preferred form the or at least one of the annotation fields is associated with a user identifier.

This association in one form allows annotations to record the submitter and time and date of that submission.

In another form the association of annotation fields with the user identifier enables the user to view annotation fields that are associated with that user. This means that those annotation fields associated with the user can be displayed to the associated user and not to any other user. This permits a user to maintain a private set of annotations. > ..

It is also envisaged that the user be permitted to make modifications directly to one or more of the annotation fields that are associated with that user identifier. Prior art techniques require a request to be put to a database manager who then makes the required changes. Those required changes are then made available to all other users.

In one preferred form the user is able to select one or more subject genetic sequences to search using a query genetic sequence. In a further preferred form, the user is able to transmit, for example by FTP, at least one subject genetic sequence in order to make that subject genetic sequence available for searching with the query genetic sequence.

In a further preferred embodiment, the user maintains the query genetic sequence in computer memory. Computer memory includes for example a data cache or searchable hard disk. The query genetic sequence is able to be searched for one or more sub-sequences of the or at least one of the subject genetic sequences. A search result is then determined based at least partly on the results of searching the query genetic sequence for the one or more sub-sequences. The results are returned to the user as search results.

A user search in which a subject genetic sequence and a query genetic sequence are each searched for sub-sequences of the other are known as an "all by all search". It is envisaged that the user be provided with the facility to conduct all by all searches. One example of the use of an all by all search would be to search all possum genomic reads by all possum genomic reads to cluster them into related groups. A further example would be to search all lactation genes from all mammals (for example possum, mouse, human and cow) by way of an all by all search to cluster them into functional groups.

It is envisaged that customers with heavy usages can purchase a discounted package of usage fees that also could be a fixed rate for a defined period of time.

Suitable protection mechanisms are in place to prevent individual users accessing the search results of other users. Search engine 105 does not store the results of the searches for a longer period than is strictly necessary to return the search result to the user.

The foregoing describes the invention including preferred forms thereof. Modifications and improvements as would be obvious to those skilled-in the art are intended to be incorporated in the scope hereof as defined by the accompanying claims.

Claims

WHATWE CLAIM IS:

1. A method of searching one of more subject genetic sequences maintained in at least one database, the method comprising:

receiving a user identifier from a user; ι.

checking the received user identifier against a plurality of stored user identifiers;

checking an authorisation record of the user identifier;

on detecting a match between the received user identifier and one of the stored user identifiers, receiving a query genetic sequence;

searching the or at least one of the subject genetic sequences in the database(s) for one or more sub-sequences of the query genetic sequence;

determining a search result based at least partly on the results of searching the database(s) for the one or more sub-sequences;

returning die search result to the user; and

debiting the user for the search result.

2. The method of claim 1 further comprising associating one or more annotation fields with the or at least one of the subject genetic sequences.

3. The method of claim 2 further comprising associating the or at least one of the annotation fields with the user identifier.

4. The method of claim 3 further comprising displaying to the user the or at least one of the annotation fields associated with the user identifier.

5. The method of claim 3 of claim 4 further comprising receiving from the user modifications to the or at least one of the annotation fields associated with the user identifier.

6. The method of any one of the preceding claims further comprising receiving a user selection of the or at least one of the subject genetic sequences.

7. The method of any one of the preceding claims further comprising receiving the or at least one of the subject genetic sequences.

8. The method of any one of the preceding claims further comprising:

searching the query genetic sequence for one or more sub-sequences of die or at least one of the subject genetic sequences;

determining a search result based at least partly on the results of searching the query genetic sequence for the one or more sub-sequences; and

returning the search result to the user.