CN100350406C - Method, system and computer software for providing genomic web portal - Google Patents

Abstract

Systems, methods, and computer program products are described that process inquiries or orders for purchasing biological equipment, materials, or related reagents. In some implementations, a user selects a probe set identifier that identifies the set of microarray probe sets capable of detecting biomolecules. The corresponding gene or EST is identified and associated therewith with relevant product data, and the product data is provided to the user. In addition, users can select products to purchase based on product data. If so, the user's account may be adjusted based on the purchase order. In the same or other implementations, a local genome database is periodically updated. Responsive to a user selection of a probe set identifier, relevant data corresponding to a gene or EST is provided to the user from the local genome database.

Description

Method and system for providing GeneNet portal

related application

This application claims priority to U.S. Provisional Patent Application Serial No. 60/178,077, entitled "Method, System, and Computer Software for Providing GeneNet Portal," filed January 25, 2000, It is hereby incorporated by reference in its entirety for all purposes.

Background technique

The present invention relates to the field of bioinformatics, in particular to a computer system, method, and product for providing gene information on a network such as the Internet.

Research in molecular biology, biochemistry, and many health-related fields requires extensive organization and analysis of complex data generated by new experimental techniques. These tasks are pursued through the rapidly developing field of bioinformatics. See, eg, Fundamentals of Bioinformatics by H. Rashidi and K. Buehler: Application in Biological Science and Medicine (CRC Press, London, 2000); Bioinformatics: Analysis of Genes and Proteins ( A Practical Guide to the Analysis of Gene and Protein ) (BFOuelette and ADBzevanis, eds., Wiley & Sons, Inc., 1998), the entire contents of which are hereby incorporated by reference. Broadly speaking, a field of bioinformatics is the application of computational techniques to large genetic databases, usually distributed over and accessed over a network such as the Internet, in order to describe gene structure and/or location, protein function, and Relationships between metabolic processes.

Contents of the invention

The expanded use of microarray technology is a driving force for the advancement of bioinformatics. In particular, microarrays and related instrumentation and computer systems have been developed rapidly and collect data on the expression of genes or expressed sequence tags (ESTs) in tissue samples on a large scale. Among other things, the data can be used to study genetic characteristics and detect mutations in genes and other diseases or conditions. More particularly, data obtained through microarray experiments are valuable for research because, among many other reasons, many disease states are characterized essentially by differential expression levels of various genes, also by the presence of Alterations in the copy number of inherited DNA or through changes in the level of specific gene transcripts (eg, by initiation control, provision of RNA precursors, or RNA processing). Thus, for example, researchers use microarrays to answer the question: Which gene is expressed in the cells of a malignant mass, but not in healthy tissue or tissue treated according to a particular condition? Which gene or EST is expressed in a particular tissue construct but not in others? Which gene or EST is expressed in a particular species but not in others? However, data collection is only a first step in answering these and other questions. Extracting biologically meaningful information from the large amount of data generated by microarray technology, and designing improved experimental equipment, is a major challenge for researchers. What is needed now is to provide researchers with advanced tools and information to perform these tasks.

Systems, methods and computer program products are described herein addressing these and other needs. In some implementations, a web portal handles inquiries or orders related to the purchase of biological equipment or material, or related reagents. The user selects a "probe set identifier" (a broad term described below), which can be associated with a probe set set of one or more probes. These probes are capable of detecting biomolecules. These biomolecules include, but are not limited to, nucleic acids including DNA expression or mRNA transcription and/or expression of corresponding genes (for convenience, the nucleic acid is hereafter simply referred to as "mRNA transcription"). Corresponding genes or ESTs are identified and correlated with the relevant data provided to the user. In some aspects, users may choose to purchase data-based products. If the user decides to make a purchase, the user's account is adjusted according to the purchased order.

An advantage of these implementations is that, based on the results from an initial experiment, product recommendations for the experiment can be presented to a user. These preliminary results are indicated by the user's choice of probe set identifiers, eg, by specifying those probe set identifiers corresponding to probes expressed as relatively high-order differentials in the control and experimental samples.

In the same or other implementations, a local genome database is periodically updated. In some aspects, such updates can be made from a remote database. In response to a user selection of the probe set identifier, data about the gene or EST is provided to the user from the local genome database. In another aspect, data about genes or ESTs is provided to the user from the local genetic database in response to user selection of a gene and/or EST identifier.

Some advantages of these implementations include the ability for a user to initiate a data request based on the results of an experiment. As just one example, the user indicates these results by selecting probe set identifiers that correspond to relatively high differential gene expression. Furthermore, these implementations may also have advantages in that the genetic data is locally available at the time of the user's request and generally need not involve interrogating a remote database in response to the user's request. Instead, query the remote database periodically, for example one week. Thus, even if the user's selection includes a large number of probe set identifiers, expressions or differentials specifying a large number of genes and ESTs, a response can be quickly provided to the user from the local gene database. Effective delays are usually avoided due to multipathing or batching of queries to remote databases.

Additionally, in the foregoing and other implementations, a method is described by which a user places a computer-implemented inquiry or order regarding the purchase of one or more products. A user selects a first set of probe set identifiers, and the selection is sent via the Internet to a portal system capable of having data associated with one or more genes or ESTs corresponding to the user selected probe set identifiers. The user receives relevant data from the portal system. The user may select some or all of the data or otherwise express an additional desire to purchase products related to the data. If the user chooses to purchase a product, the user's account is adjusted accordingly.

In some implementations, a system is described for providing data about one or more genes or ESTs, where each gene or EST has at least one probe set corresponding to a probe set identified by a probe set identifier, and capable of detecting a biological molecule. The biological molecule can be a nucleic acid or an mRNA transcript of a corresponding gene. As noted above, the one or more probe set identifiers may include a gene or EST identifier, such as an accession number. The system includes an input manager that receives a user selection of a first set of probe set identifiers; a gene determiner that identifies genes or ESTs corresponding to the probe set identified by the first set of probe set identifiers; a A correlator, which correlates genes or ESTs with the data; and an output manager, which provides the data to the user. The input and output managers of these instruments can be coupled to users via the Internet.

The first set of probe set identifiers may be a subset of the probe set identifiers of the second set of probe sets having the ability to detect the expression or differential of a corresponding gene or EST. For example, the subset can be selected by the user through a graphical user interface provided by a probe array software application. This selection can be made, for example, by drawing a circle around outliers in a scatterplot representing probe settings, wherein the outliers represent probe settings with relatively high order differentials. As many other examples are possible, the user can select subsets of the highlighted entries by probe setting identifiers in a command form.

Typically probe arrangements are placed on one or more probe arrays, which, as mentioned, can be any of various types of microarrays, such as those integrated or spot arrays using VLSIPS ^(TM) technology (described below). Thus, the term "probe arrangement" is generally understood to include not only a comprehensive set of probes, eg according to the VLSIPS ^™ technique, but also one or more spots deposited according to various spot array techniques (also described below). These spots are for example oligonucleotides or other cDNA clones or PCR products generated from those clones. This data may include product data regarding availability, price, composition, suitability, or orders for various products including biological devices or substances, or a reagent, which may be used in biological devices or substances, or additional information such as Nucleotide or protein sequence information or localized or functional annotation information. As some examples, the device may be a probe array or a microscope slide, or the substance may be clones, oligonucleotides, antibodies, or proteins.

Other implementations are directed towards methods for providing data about one or more genes or ESTs, each gene or EST having at least a corresponding probe set identified by a probe set identifier, and capable of biomolecular detection. A biomolecule may be a nucleic acid or an mRNA transcript of a corresponding gene. The method includes the steps of: receiving a user selection of a first set of probe set identifiers; identifying genes or ESTs corresponding to the probe sets identified by the first set of probe set identifiers; correlating the genes or ESTs with the data; and Provide data to users. Still other instruments are directed to a computer program product for carrying out the aforementioned method.

Additional implementations are directed to a method for placing a computer-implemented inquiry or ordering order for the purchase of one or more products. The method includes the steps of: receiving, at a user computer, a user selection of a first set of one or more probe set identifiers, wherein each probe set identifier identifies a probe set capable of detecting expression of a corresponding gene; selection is provided via the Internet to a portal system capable of correlating the data with one or more genes or ESTs corresponding to the probe set identified by the first set of probe set identifiers; and receiving the associated data. In addition, users can also select product data for purchase.

Another implementation is directed towards a system for providing data about one or more genes or ESTs, each of which has at least one corresponding probe set identified by a probe set identifier, and is capable of detecting a Biomolecules. A biomolecule can be a nucleic acid or an mRNA transcript corresponding to a gene. The system includes a database manager which periodically updates a local gene database comprising relevant gene or EST data; an input manager which receives a user-selected probe set identifier; a user service manager which corresponds to the probe set Set identifiers to construct local gene database data about genes or ESTs; and an output manager to provide the data to users.

In the implementation described above, the database manager may update the local gene database periodically, e.g., once a week, with sequence data, foreign structure or localization data, splice variant data, marker structure or localization data, polymorphic data, homology data, protein homology classifications data, pathway data, alternative gene nomenclature data, bibliographic data, annotation data, other genomic or proteomic data, or any combination thereof. This updating can be accomplished through periodic communication with a remote database, possibly over the Internet. Can include any of hundreds or thousands of public or proprietary remote databases such as GenBank, GenBankNew, SwissPort, GenPept, DB EST, Unigene, PIR, Prosite, PFAM, Prodom, Blocks, PDB, PDBfinder, EC Enzyme, Kegg Pathway, Kegg Ligand, OMIM, OMIM Map, OMIM ALLele, DB SNP, and/or PubMed. While the database manager periodically communicates with the remote database, typically (but not necessarily) not responding to a user request, the input manager typically (but not necessarily) dynamically receives the user's choice of probe setting identifier . The word "dynamic" as used herein is intended to mean responding to a user's query in real time.

In another implementation, a system for providing product data, which may include biological product data, is described. The system has an input manager that receives a gene, EST, and/or probe set identifier from a user. For example, a user may specify one or more genetic access numbers. Additionally, the system has a user services manager that sets identifiers with one or more product data associated or linked genes, ESTs, and/or probes. The customer service manager may also optionally cooperate with a database manager to obtain product data from one or more local and/or remote databases or other local or remote data sources, such as from a web page. In addition, an output manager is included in the system to provide product data to users. In some aspects, user accounts may be adjusted based on purchases, or for users that are dependent on vendors, a vendor account may be adjusted. Receiving information from users and providing information to users can take place over a network, such as the Internet. In another aspect, a method for providing product data, eg, biological product data, is described. The method comprises the steps of: receiving a gene, EST, and/or probe set identifier from a user; correlating the gene, EST, and/or probe set identifier with one or more product data; receiving from a local and/or obtaining the product data from a remote database or other local and/or remote data source; and providing the product data to the user. The method optionally includes adjusting a user account based on purchases, or adjusting a vendor's account for users dependent on the vendor.

Another aspect is a system for providing data about one or more genes or EST products. Each gene or EST has at least a corresponding probe set identified by a probe set identifier and is capable of detecting a biomolecule. The system includes an input manager that receives one or more probe set identifiers; a correlator that correlates the probe set identifiers with one or more first sets of product data; and an output manager that provides the first A set of data to the user. Another aspect is a system for providing product data about one or more genes or ESTs. The system includes an input manager that receives one or more gene and/or EST identifiers; a correlator that correlates the identifiers with a first set of one or more product data; and an output manager that provides the first Group data to the user.

An additional aspect is a method for providing data about one or more genes or EST products. Each gene or EST has at least a corresponding probe set identified by a probe set identifier and is capable of detecting a biomolecule. The method includes the steps of receiving one or more probe set identifiers; correlating the probe set identifiers with a first set of one or more product data; and providing the first set of data to a user. Another aspect is a method of providing data about one or more genes or EST products. The method includes the steps of receiving one or more gene and/or EST identifiers; correlating the identifiers with a first set of one or more product data; and providing the first set of data to a user.

According to another aspect of the invention, a system for providing data about one or more genes or EST products is described. The system includes receiving means for receiving one or more gene or EST identifiers on the Internet; correlating means for correlating one or more product data with the gene or EST identifiers; and providing means for providing Product data to users.

According to another aspect of the present invention, a system for providing product data about one or more genes or ESTs is described, wherein each gene or EST has at least a corresponding probe set identified by a probe set identifier, and be able to detect a biomolecule. The system includes: receiving means for receiving from a user a selection of a first set of one or more probe setting identifiers; correlating with the setting identifier; and providing means for providing the first set of data to the user.

In an additional aspect, a system for providing data about one or more genes or ESTs is described, wherein each gene or EST has at least one corresponding probe set represented by a probe set identifier, and is capable of Detect biomolecules. The system includes updating means for periodically updating a local gene database comprising relevant gene or EST data; input management means for receiving from a user a selection of a first set of one or more probe set identifiers; data managing means for periodically updating the first set of data from the local gene database regarding genes or ESTs corresponding to the first set of probe set identifiers; and providing means for providing the first set of data to a user.

The implementations described above are not necessarily mutually inclusive or exclusive and can be combined in any way, non-conflicting and variously possible, whether they appear in the same or different aspects or implementations. The description of one implementation is not intended to limit other implementations. Furthermore, any one or each of the functions, steps, operations, or techniques described elsewhere in this specification may be combined in alternative implementations with any one or more of the functions, steps, operations, or techniques described in the Summary. Therefore, the above-mentioned implementation manners are only examples and not intended to be limiting.

Description of drawings

The above and other advantages will become more apparent from the following detailed description taken in conjunction with the accompanying drawings. In the drawings, like reference numbers indicate like structural or method steps, and the leftmost one or two digits of a reference number indicate the number of the figure in which the referenced element first appears (e.g., element 180 appears for the first time in FIG. 1 and unit 1020 appears for the first time in FIG. 10). In function block diagrams, rectangles typically represent functional units, parallelograms typically represent data, rectangles with curved sides typically represent stored data, rectangles with a pair of double borders typically represent predefined functional units, and trapezoids typically represent manual operations . In method flow diagrams, rectangles generally represent method steps and diamonds generally represent decision units. However, all of these idioms are intended to be typical or exemplary only, and not intended to be limiting.

Figure 1 is a functional block diagram of a probe array analysis system including a scanner and a computer system on which a computer application program can be executed for providing probe set identifiers and for receiving needles for processing the probes User choice of setting identifier;

Figure 2 is a functional block diagram of one embodiment of a probe array analysis application, as shown for the application stored in the system memory of the computer system of Figure 1;

Fig. 3 is a functional block diagram of a conventional system for obtaining genetic information via the Internet;

Figure 4 is a functional block diagram of one embodiment of a gene portal coupled to remote databases and web pages via the Internet and to customers, comprising a network with the user computer system of Figure 1;

Figure 5 is a functional block diagram of an embodiment of the gene portal of Figure 4, including a database server, a portal application computer system, and an exemplary embodiment of a portal-side Internet server;

Figure 6 is a simplified diagram representing an embodiment of a computer application platform for implementing the gene portals of Figures 4 and 5 in conjunction with clients such as those shown in Figure 4;

Figure 7 is a flow chart of a method of an embodiment for providing a user with gene product information related to gene expression, or differential expression, experimental results;

Figure 8 is a functional block diagram of one embodiment of a user service manager application that may be executed on the portal application computer system of Figure 5;

Fig. 9 is a simplified diagram, representing an embodiment of a gene or probe setting identifier to a database, for example, the user service manager in Fig. 8 can be combined with the method in Fig. 7;

Figure 10 is an embodiment of a graphical user interface that may be generated by a probe array analysis application of Figure 2; and

FIG. 11 is another example illustrating a user interface that may be generated by a probe array analysis application of FIG. 2 .

Detailed ways

Systems, methods and computer products are now described with reference to an example embodiment of the Gene Portal 400 . Portal 400 is shown in an Internet environment in Figure 4 and is illustrated in more detail in Figures 5-11.

In a typical implementation, portal 400 can be used to provide a user with information about results from experiments with probe arrays. The experiment typically involves detection of hybridization of probe-target pairs using a scanning device, and analysis of the detected hybridization by various software applications, now described with reference to FIGS. 1 and 2 .

Probe Array 103

Various techniques and technologies can be used to deposit or synthesize dense arrays of biological materials on a substrate or support. For example, Affymetrix(R) GeneChip(R) arrays, manufactured by Affymetrix Inc. of Santa Clara, California, are synthesized according to a technique sometimes referred to as VLSIPS ^(TM) (Very Large Scale Immobilized Polymer Synthesis). Some aspects of VLSIPS ^™ technology are described in the following U.S. Patents: 5,143,854 (Pirrung, et al.); 5,445,934 (Fodor, et al.); 5,744,305 (fodor, et al.); 6,022,963 (Mcgall, et al. ); and 6,083,697 (Beecher, et al.) at. The entire contents of these patents are hereby incorporated by reference. The probes for these arrays consist of oligonucleotides which are synthesized by methods which include the steps of activating a region of the substrate and then contacting the substrate with a solution of selected monomers. The activated areas are revealed through a mask with a light source, the same photography technique used in the manufacture of integrated circuits. Other areas of the substrate remain inactive because the mask blocks illumination from them. By repeatedly activating different sets of regions and exposing the substrate to different monolithic solutions, different arrays of polymers were created on the substrate. Various other steps are used in various implementations of these methods, such as washing unreacted monolithic solutions from the substrate.

These probes are typically used in conjunction with labeled biological samples, such as cells, proteins, genes or ESTs, other DNA sequences, or other biological elements. These samples, referred to herein as "targets," are processed so that they are spatially associated with defined probes in the probe array. For example, one or more chemically labeled biological samples, ie, targets, are distributed on the probe array. Some targets hybridize to at least spatially compensated probes and remain in place of the probes, while non-hybridized targets are washed away. These hybridized targets with their "labels" or "tags" are thus related to the targets of the compensation probes. Hybridized probes and targets may sometimes be referred to as "probe-target pairs." Detecting these pairs can serve various purposes, such as determining whether a nucleic acid of interest has a nucleotide sequence that is identical or different to a particular reference sequence. See, eg, US Patent No. 5,837,832, relating to and incorporating the above. Other uses include gene expression monitoring and assessment (see, e.g., U.S. Patent No. 5,800,992 (Fodor, et al.); U.S. Patent No. 6,040,138 (Lockhart, et al.); and International Application No. PCT/US98/15151, Published as WO99/05323 (BALABAN, et al.)), genotype (US Patent No. 5,856,092, Dal, et al.), or detection of other nucleoproteins. The '992', '138', and '092 patents mentioned above, as well as publication WO99/05323, are hereby incorporated by reference in their entirety for all purposes.

Other techniques exist for depositing probes on a substrate or support. For example, "arrays of dots" that are commercially fabricated on microscope slides. These arrays include liquid spots that contain potentially varying compositions and concentrates of biological material. For example, a spot in an array may comprise a few short strands of oligonucleotides in an aqueous solution, or it may comprise highly concentrated strands of synthetic proteins. The Affymetrix(R) 417 ^™ Arrayer is a device for depositing densely packed arrays of biological material on a microscope slide according to the techniques and methods described in PCT Application PCT/US99/00730 (International Publication No. WO99/36760) described, the entire contents of which are hereby incorporated by reference. In addition, other techniques exist for producing spot arrays. For example, US Patent nO. 6,040,193 (Winkler, et al.) formulates drops for treatment to produce dotted arrays. The '193 patent, and US Patent No. 5,885,837 (Winkler) also describe the use of microchannels or dimples on a substrate or on blocks loaded onto a substrate to synthesize arrays of biomaterials. These patents further describe the isolation of reactive regions of a substrate from each other by inert regions and test points on the reactive regions. The entire contents of the '193 and '837 patents are hereby incorporated by reference. Other techniques are based on jetting biological material to form a dotted array. Other implemented ejection techniques may use devices such as hydrometers or pressure electronic pumps to propel the biomaterial. Various other techniques are currently available for synthesizing, depositing, or localizing biological materials on or within a substrate.

In order to ensure proper interpretation of the term "probe" as used herein, attention should be paid to contradictory conventions appearing in the relevant literature. The word "probe" used in some articles does not refer to biological material synthesized on a substrate or deposited on a slide as described above, but is referred to herein as "target". To avoid confusion, the term "probe" is used herein to refer to probes such as those synthesized according to the VLSIPS ^™ technique; deposited biological material to generate dotted arrays; and synthesized, deposited, or localized samples to form arrays according to other present or future technologies. Thus, for convenience, microarrays formed according to any of these techniques may be referred to hereinafter generally and collectively as "probe arrays". Furthermore, the term "probe" is not limited to probes immobilized in an array format. On the contrary, for other parallel experimental facilities, the described functions and methods are also useful for providing genomic information and smart e-commerce. For example, these functions and methods can be applied to probe set identifiers, identifying immobilized probes on and in beads, in optical fibers, or other substances or media.

Typical probes are capable of detecting the expression of a corresponding gene or EST by detecting the presence or distribution of transcripts present in the target mRNA. This detection can be done in turn by detecting tagged cRNA derived from cDNA derived from mRNA in the target. Typically, a probe set contains subsequences in uniquely transcribed regions and does not correspond to a complete gene sequence. The word "set" as used generally herein refers to one or more; for example, a probe set may consist of one or more probes, and a set of probe set identifiers may consist of one or more probe set identifiers .

Scanner 190

Figure 1 is a functional block diagram of a system particularly useful for analyzing, among other things, an array of probes hybridized to a tagged target. Hybridization-representing probe array 103 of FIG. 1 may comprise any type of probe array, as described above. The labeled targets in the hybridization probe array 103 can be detected using various commercial equipment, hereafter referred to as "scanners" for convenience. One example device shown in FIG. 1 is scanner 190 . Scanners image targets by detecting fluorescent or other radiation from tags, or by emitted, reflected, or scattered radiation. For convenience, hereafter these processes generally focus on detection simply referred to as "radiation" using various detection schemes. Depends on the type of radiation and other factors. A typical approach is to use light and other elements to provide excitation light and selectively collect radiation. Additionally, various photodetector systems using photodiodes, charge-coupled devices, photomultiplier tubes, or similar devices to register collected radiation are typically included. For example, one scanning system using fluorescent tags is described in US Patent No. 5,143,854, incorporated herein by reference. Other scanners or scanning systems are described in U.S. Patent Nos. 5,578,832; 5,631,734; 5,834,758; 5,981,956 and 6,025,601, and in PCT Application PCT/US99/06097 (publication number WO99/47964), the contents of which are incorporated herein by reference for all purposes. all content.

Scanner 190 provides data representing the intensity (and possibly other characteristics, such as color) of the detected radiation, as well as the location on the substrate where the radiation was detected. The data is typically stored in a memory device, such as system memory 120 of user computer 100, in the form of a data file. One type of data file, such as image data file 212 shown in FIG. 2, generally includes intensity and position information for elements corresponding to sub-regions of the scanned substrate. The term "elemental" in the text means the intensity of radiation from the region, and/or other characteristics, each representing a single value. When displayed as an image for viewing or manipulation, the element's picture elements, or pixels, generally represent that information. Thus, for example, a pixel has a single value representing the intensity of a subarea element of the substrate as radiation is scanned from the substrate. The pixel may also have additional values representing additional characteristics, such as color. For example, a subregion of a scanned element in which high-intensity radiation is detected may be represented by a pixel with high intensity (hereinafter, referred to as a "bright" pixel), and low-intensity radiation may be represented by a low-intensity (a "dim" pixel ) to represent a pixel. Alternatively, a pixel's color value can be made to represent intensity, color, or other characteristic of the detected radiation. Thus, an area of high luminance radiation can be displayed as red pixels and an area of low luminance radiation can be displayed as blue pixels. As another example, detected radiation of one wavelength on a particular subregion of the substrate can be represented as red pixels, and detected radiation of a second wavelength on another subregion can be represented by a near blue pixel. Pixel representation. Many other solutions are known.

Probe Array Analysis Applications 199

Typically, one can examine a printed or displayed image constructed from data in an image file and can identify cells that are bright or dim, or otherwise identified by a pixel characteristic such as color. However, this frequently requires providing this information in an automated, quantifiable, and repeatable manner that is compatible with various image processing and/or analysis techniques. For example, information can be provided for processing by computer application regarding the locations at which hybridized targets are detected using known locations at which known identical probes were synthesized or deposited. Information such as nucleotides or monomers of the target DNA or RNA can then be derived. Techniques for making these derivations have been described, for example, in US Patent No. 5,733,729 (Lipshutz), and US Patent No. 5,837,832, the entire contents of which are hereby incorporated by reference for all purposes.

A variety of computer software applications are commercially available for controlling scanners (and other hybridization-related instruments, such as hybridization chambers), and for obtaining and processing image files provided by scanners. Examples are the Jaguar ^™ application from Affymetrix Corporation, described in this regard in U.S. Provisional Patent Application Serial No. 60/226,999, filed August 22, 2000, and the Microarray program application from Affymetrix, described in this regard at U.S. Provisional Patent Application Serial No. 60/220,587, filed July 25, 2000. Processed image files produced by these applications are often further processed to extract additional data. In particular, data mining software applications are often used to aid in the identification and analysis of patterns of biological interest or the degree of hybridization of probe sets. The Affymetrix(R) data mining tool is an example of a software application of this type. In addition, software applications are used to store and manage the large volumes of data typically generated by probe array experiments and through the image processing and data mining software described above. An example of such data management applications is the Affymetrix(R) Laboratory Information Management System (LIMS), the subject of which is described in US Provisional Patent Application Serial No. 60/220,645, filed July 25,2000. In addition, various property databases accessed by database management software, such as the Affymetrix(R) EASI (Expression Analysis Sequence Information) database and database software, provide the researcher with the relationship between probe sets and gene or EST identifiers. All patent applications mentioned in this paragraph are hereby incorporated by reference in their entirety.

For ease of reference, these types of computer software applications (i.e., for acquiring and processing image files, data mining, data management, various databases, and other applications related to probe array analysis) are shown in Figure 1 Typically centrally represented as an analysis application 199 . FIG. 2 is a functional block diagram of probe array analysis application 199 , as an example program stored for execution (corresponding to executable code 199A of application 199 ) in system memory 120 of user computer 100 of FIG. 1 .

As should be clear to those skilled in the art, it is not required that the application 199 be stored on and/or executed from the computer 100; rather, some or all of the application 199 may be stored on and/or executed from an application server or other computer platform. To execute, they are connected to the computer 100 in a network. For example, it is especially advantageous for applications involving large-scale database operations, such as Affymetrix(R) LIMS or Affymetrix(R) Data Mining Tools (DMT), to be executed from a database server, such as user database server 412 of FIG. Alternatively, LIMS, DMT, and/or other applications may execute from computer 100, but some or all of the databases of those applications running thereon may be stored for public access on server 412 ( Possibly along with a database management program, such as the Oracle(R) 8.0.5 database management system from Oracle Corporation). Such network arrangements can be implemented according to known techniques using commercially available hardware and software, such as those available for a local or wide area network. Shown in Figure 4 is a local area network connecting user computer 100 to user database server 412 (and to client Internet client 410, which may be the same computer) via network cable 480. Likewise, scanner 190 (or scanners) may be made available via cable 480 to a user's network for the purpose of controlling scanner 190 and receiving data input therefrom.

Referring again to FIG. 2, executable application programs 199A generate various types of data in various formats, those shown being merely examples. For convenience, the term "file" is used herein to refer to data generated or used by the executable application 199A, but any type of data for storage, transfer, and/or or manipulated data. In the example of the figure, data analysis program 210 receives image data file 212 from scanner 190 and generates element intensity file 216 therein. File 216 for this example contains for each probe scanned by scanner 190 a single value representing the pixel intensity measured by scanner 190 for that probe. Thus, this value is a measure of the distributed amount of labeled mRNA present in the target hybridized to the corresponding probe. Many such mRNAs can be present in each probe, as a probe can include, for example, millions of oligonucleotides designed to detect nRNA.

In the illustrated example, the probe array data analysis program 210 generates an experiment information file 213 , which is typically entered by the user 101 , containing information about the experiments, samples, and probe arrays. A primary function of the data analysis program 210 of this example is to analyze file 216 and/or file 212, possibly along with information from file 213 and internal library files (not shown), which specify the sequence and location of probes and controls. detail. The purpose of a program such as the data analysis program 210 of this example is generally to provide information such as degree of hybridization, absolute and/or differential (over two or more experiments) expression, genotype comparison, polymorphism and variant detection , and the results of other analyses. In this example, file 215 represents the analysis output of such data analysis program 210 . Data analysis program 210 may process file 215 to generate report file 214, which may respond to user 101 requests regarding form and content. It should be clear to those of ordinary skill in the art that the aforementioned and hereinafter described files, reports, and data representations generated by the exemplary data analysis program 210 are merely exemplary and can be processed, combined, and arranged in many other ways , and/or data representing descriptions and other data.

Additionally, data analysis program 210 generates various types of curves, graphs, tables, and other tabular and/or graphical representations of the analyzed data such as contained in file 215 . An example is shown in FIG. 10 , which shows a graphical user interface (GUI) 1000 having a discrete drawing window 1010 and a tabular window 1020 . In scatter plot window 1010, line 1011 provides a reference for the levels of differentials measured by probe set-ups in different experiments. The location of points, each representing a probe setup from one or more microarrays, along an axis specifying the expression of the probe setup in an experiment or set of experiments (e.g., experiments that measure control sampling). degree, and along the other axis, the degree of expression in another experiment or set of experiments (eg, an experiment measuring disease sampling).

In FIG. 10, the user 101 has a demarcation line 1014 around cluster points 1016 (using prior known techniques). In tabular window 1020, each probe setting corresponding to a point in window 1010 is identified and described in a separate row. In this example, and as in column 1034, the row entry includes a measure of the level of expression in a particular trial (as in column 1032), an indication of whether the expression was absent (A) or present (P ). The row corresponding to the dots, ie, the probe setting group, enclosed in the circle 1014 is highly illuminated in the window 1020 so that the user 101 can easily identify information about the selected probe setting group. Additionally, as in column 1036, each row in window 1020 includes a probe set identifier.

For example, the probe settings corresponding to rows 1021 and 1022 are highlighted to show that their corresponding points have been surrounded in window 1010 . The entries in column 1036 for these rows, ie, "M13903_at" and "M14091_at", respectively, are probe set identifiers for their corresponding probe sets. FIG. 10 thus illustrates a number of techniques by which a user 101 may select a probe setting identifier. In particular, the user 101 does this in the present example by surrounding points in window 1010 (and in this case, the selected probe setting identifier includes surrounding points) and/or by picking a row in window 1020 Select (and in this case, the selected probe set identifier includes the name in column 1036). As shown in FIG. 2 , probe set identifiers 222 represent these or other probe set identifiers that may be provided for selection by user 101 through applications such as data analysis program 210 . In addition, the convention used in the data analysis program 210 for naming probe sets of this example includes sometimes indicating the accession number of the gene or EST information corresponding to the probe set. For example, the probe set identification name "M13903_at" in row 1021 indicates the accession number of the gene or the EST corresponding to the probe set that is M13903 for that row. In other examples, the corresponding access number may be displayed directly. The facilities for these access numbers selected by the user 101 are indicated by the access numbers 124 in FIG. 2 . Although, as illustrated, the access number can function as a kind of probe set identifier (and thus the access number 124 can be considered a subset of the probe set identifier 222), for ease of illustration and discussion, They are clearly shown in FIG. 2 .

Other executable applications 199A, such as data mining tools 220 may also provide probe setup identifier 222 (optionally including access number 224 ) to user 101 . Another example is database application 230, an illustrative GUI of which is shown in FIG. The database application 230 is an application program for associated probe sets, generally identified by probe set identifiers, such as names, numbers, and/or symbols, for corresponding genes or ESTs. An example of database 230 is the EASI database application from Affymetrix, Inc. as noted above. In the example of FIG. 11 , GUI 1100 includes a query window 1110 , and a results window 1120 . As shown in FIG. 11 , the user 101 has effectively generated a query by selecting a particular probe array 1112 and a caption portion 1114 associated with the array 1112 or any probe settings associated with the array 1112 in accordance with known techniques. . Application 230 performs a search of the database (not shown), and displays the results of the query in window 1120 . As described below with respect to the database of FIG. user's query. In both cases, the results of the user query generally include an identification of the probe array satisfying the query, such as array 1122 , and a probe set identifier, such as identifiers 1124 and 1126 . As exemplified previously, the name "AF058789_at" given to the identifier 1124 may indicate the accession number or EST that is the gene set corresponding to the probe identified therein. The user 101 may highlight a probe setting identifier with a corresponding identifier 1126, such as shown in FIG. 11 . The recognized tree structure of window 1120 shows that the probe settings identified by identifier 1126 are arranged on array 1122 . Descriptive information associated with this probe setup identified by identifier 1126 is also highlighted and displayed in the same row as identifier 1126 in a tree structure.

The LIM application 225 is also shown in FIG. 2 as an exemplary example of an executable analysis application 199A. Application 225 may manage files used or generated by data analysis program 210 (e.g., files 212-216), as well as files or data generated or used by DMT 220 and other types of probe array analysis applications. The LIM 225 can store, maintain, process and display these and other data generated by one or more experimenters over time to simplify management and experiment planning and reporting of results. Based on a library database (not shown), LIM 225 may also provide SIF information represented in FIG. 2 by file 217 (described below). As described above with respect to applications 230 , files 217 may be selected or otherwise stored and maintained by portal 400 . For example, SIF information may be stored in local library database 516 and managed by database management 512, which may include a LIM such as LIM 225 or incorporate some or all of its functionality.

user computer 100

The user computer 100 shown in FIG. 1 may be a computing device specially designed and equipped to support and execute some or all of the functions of the probe array application 199 . The computer 100 may also be any various types of general-purpose computers developed now or in the future, such as personal computers, network servers, workstations or other computer platforms. Computer 100 generally includes known components such as processor 105 , operating system 110 , graphical user interface (GUI) controller 115 , system memory 120 , memory storage 125 , and input-output controller 130 . Those skilled in the relevant art will appreciate that there are many possible configurations for the elements of computer 100, and that certain components not shown may generally be included in computer 100, such as cache memory, data backup units, and many other devices. Processor 105 may be a commercially available processor, such as a Pentium ^(R) processor manufactured by Intel Corporation, a SPARC ^(R) processor manufactured by Sun Microsystems, or one of other available processors. Processor 105 executes an operating system 110, which may be, for example, a Windows ^(R) type operating system from Microsoft Corporation (such as Windows NT( ^R) 4.0 with SP6a); a Unix ^(R) or Linux type operating system available from many vendors; other or future operating systems; or some combination of them. Operating system 110 interfaces with program packages and hardware devices in a known manner, and facilitates processor 105 to coordinate and execute the functions of different computer programs written in various programming languages. The operating system 110 generally cooperates with the processor 105 to coordinate and execute the functions of the other components of the computer 100 . Operating system 110 also provides scheduling, input and output control, file and data management, memory management, and communication control and related services in full accordance with known techniques.

System memory 120 may be any known or future storage device. It includes, for example, any of commonly available random access memory (RAM), magnetic media such as hard disks or magnetic tape for resident data, optical media such as compact discs for direct-read recording, or other memory storage devices. Storage device 125 may be any known or future device, including a compact disk drive, tape drive, removable hard disk drive, or floppy disk drive. Memory storage devices 125 of this type typically read from and/or write to a program memory medium (not shown), such as a compact disk, magnetic tape, removable hard disk, or floppy disk, respectively. All of these program storage media, or others now in use or which may be developed at a later date, may be considered computer program products. Obviously, these program storage media generally store computer software programs and/or data. A computer software program, also referred to as computer control logic, is typically stored in system memory 120 and/or in this program memory device used in conjunction with memory storage device 125 .

In some embodiments, the described computer program product comprises a computer usable medium having stored thereon control logic (computer software program, including program code). When executed by processor 105, the control logic causes processor 105 to perform the functions described herein. In another embodiment, for example, certain functions are implemented primarily in hardware using a hardware state machine. Implementation of a hardware state machine such that implementing the functionality described herein will be apparent to those skilled in the relevant arts.

The input output controller 130 may comprise any kind of known device, whether manual or mechanical, whether local or remote, for receiving and processing information from a user. Such devices include, for example, modem cards, network interface cards, sound cards, or other types of controllers for any type of known input device 102 . The output controllers of the input output controllers 130 may include any known controller of a display device 180 for presenting information to a user, whether manual or mechanical, whether locally or remotely. If a display device 180 provides visual information, such information may generally be logically and/or physically organized as an array of picture elements, often referred to as pixels. Graphical user interface (GUI) controller 115 may include any kind of known or future software program for providing a graphical input-output interface between computer 100 and user 101 and for processing user input. In the illustrated embodiment, the functional units of the computer 100 communicate with each other via a system bus 104 . Some of these communications may, in various embodiments, be accomplished using a network or other types of remote communications.

It will be apparent to those skilled in the relevant art that if implemented in software, the application program 199 may be loaded into the system memory 120 and/or the memory storage device 125 via one of the input devices 102 . All or part of application 199 may also reside in read-only memory or the like on memory storage device 125 , which does not require application 199 to be first loaded via input device 102 . Those skilled in the art will appreciate that application program 199, or portions thereof, may be loaded by processor 105 into system memory 120 or cache memory (not shown), or both, for ease of execution in a known manner. .

Traditional techniques for obtaining genomic data

Several conventional methods for obtaining genomic data via the Internet are available, some of which are described in the book edited by Ouelette and Bzevanis, incorporated above by reference. Figure 3 is a functional block diagram showing a simplified example. As shown in FIG. 3, user 101 may consult any of a number of public or other materials to obtain access number 224'. As indicated by manual operation 312, user 101 accesses the National Book of Medicine and National Institute of Health (Internet URL http://www.ncbi.nlm.nih.gov as accessible as of January 2001) via any web browser. The Internet web site of the National Center for Biotechnology Information (NCBI) of the library initiates the request 312. In particular, the user 101 has access to the Entrez search and retrieval system, which provides information from various databases at NCBI. These databases provide information on nucleotide sequences, protein sequences, macromolecular structures, whole genomes, and published data related thereto. Exemplarily assume that user 101 enters NCBI Entrez nucleotide database 314 in this manner and receives information including gene or EST sequences 316 . In particular, if the accession number 224' represents a large number (e.g., a hundred) of ESTs or genes of interest, as is the case when analysis of probe array experiments can easily be done, the operational tasks described so far may take a lot of time, perhaps few Hour.

User 101 typically copies sequence information from sequence 316 and pastes this information into available Accessed within the HTML file. This user-initiated operation, represented by batch BLAST request 322 of FIG. 3, can also be time-consuming and lengthy if it involves many sequences. BLAST, short for Basic Local Location Search Tool, is well known in the art and consists of a similarity search program that uses a heuristic algorithm to search against both protein and DNA sequence databases to find a local location. For example, user 101 may perform a BLAST search using the "blastn" nucleotide sequence database. The results of this batch of BLAST searches represented by similar nucleotide and/or protein sequence data 326 may not be feasible for user 101 for many hours. The user 101 can then initiate the comparison and estimation 332, either manually or using a variety of software tools. Then the user 101 can report a report 334 to explain the discovery and location strategy of the search and the requirements for the next step of the experiment

Input from user 101 to genome entry 400

FIG. 4 is an exemplary functional block diagram illustrating configurations that can be connected to the GenomeNet portal 400 by the user 101 . It should be understood that FIG. 4 is simplified and illustrative only and that many implementations and variations of the network and Internet connections shown in FIG. 4 will be apparent to those of ordinary skill in the art.

User 101 utilizes user computer 100 and analysis application 199 as described above (including generating and/or accessing some or all of files 212-217). As shown in FIG. 4 , in this example, files 212 - 217 are maintained on user database server 412 to which user computer 100 is coupled via network cable 480 . Computers 100', 100", and other users' computers on a local area network or a wide area network including an intranet, the Internet, or any other network may also be coupled to server 412 via cable 480.

It should be understood that cable 400 is merely representative of any type of network connectivity, which may include cables, transmitters, repeaters, network servers, and many other components not shown but apparent to those of ordinary skill in the relevant arts. Via the user computer 100, the user 101 can operate a web browser provided by the client Internet client 410 to communicate with the portal 400 through the Internet 499. Portal 400 may be similar to other users and/or network communications of users via Internet 499, as represented by Internet clients 410' and 410".

As previously described, the information provided to portal 400 by user 101 typically includes one or more "probe set identifiers." These probe set identifiers are typically brought to the attention of the user 101 as a result of experiments performed on the probe array. For example, the user 101 may select those probe set identifiers that enable identification of microarray probes that allow detection of mRNA transcript representations from corresponding genes or ESTs of particular interest. As is well known in the art, an EST is a fragment that does not fully characterize a gene sequence, whereas a gene sequence is usually completely and adequately characterized. The word "gene" is used here generally to refer to the full size of the known sequence of a gene, as well as to a gene that can be deduced computationally. In certain implementations, the sequences detected by the array representing the specificity of these genes or ESTs can be referred to as "Sequence Information Fragments (SIF)" and can be recorded in "SIF files" as described above with respect to LIMS 225 operations. In particular implementations, a SIF has been considered to better represent the portion of the sympathetic sequence transcribed from an mRNA of a given gene or EST. The consensus sequence may be obtained by comparing and grouping ESTs, and may also be obtained by comparing ESTs with genomic sequence information. A SIF is part of the sympathetic sequence specifically designed for probes on the array. With respect to the operation of web portal 400, it is assumed that certain microarray probe arrangements can be designed to detect the expression of genes based on EST sequences.

As noted above, the term "probe set" generally refers to one or more probes from an array of probes on a microarray. For example, in an Affymetrix ^(R) GeneChip ^(R) probe array, where probes are synthesized on a substrate, the probe set may consist of 30 or 40 probes, typically half of which are controlled. These probes collectively or in different combinations of some or all of them are considered to represent the expression of a gene or EST. In a site-directed probe array, one or more spots may likewise constitute a "probe set".

The term "probe set identifier" is used broadly herein, where many types of such identifiers can and will be included within the meaning of this term. One type of probe set identifier is a name, number, or other symbol assigned for the purpose of identifying a probe set. This name, number or symbol can be, for example, arbitrarily assigned to the probes by the manufacturer of the probe array. For example, the user may select a probe set identifier of this type by highlighting or typing the name. Another type of probe setup that is contemplated here is a graphically represented probe setup. For example, those points can be displayed on a scatterplot or other schematic, where each point represents a probe setting.

Typically, the location of the point on the graph represents the strength of the signal from the mixed, labeled, target (described in more detail below) in one or more experiments. In this manner, the user may select a probe setting identifier by tapping, drawing a circle around it, or selecting one or more points. In conjunction with the operation of the data analysis program 210, and more specifically, with respect to the user 101 drawing the circle 1014 around the scatter plot, and/or selecting the name or access number associated with the highlighted row 1021 or 1022 Examples of the above options are provided in combination. Other examples are provided above with respect to row 1126 selected by user 101 in a database that correlates probe sets with access number and other genomic information.

Another type of probe set identifier, as the term is used herein, includes nucleotide sequences. For example, it is illustratively assumed that a particular SIF is a single sequence of 500 bases that is part of a consensus sequence or specimen sequence collected from EST and/or genomic sequence information. Assume further that one or more probe settings are designed to be representative of the SIF. Therefore, a user specifying all or part of a 500-base sequence can be considered to already have all or some of the corresponding probe sets. As a further example, a user may specify a portion of a 500-base sequence, which may be unique to a SIF, or which may also identify another SIF, EST, group of ESTs, consensus sequences, and/or groupings of genes. In that case, the user has specified probe set identifiers for one or more genes or ESTs. In another variation, it is illustratively assumed that a particular SIF is part of a particular sympathetic sequence. Assume further that the user specifies that a portion of the sympathetic sequence is not included in the SIF, but is unique to the sympathetic sequence or gene or EST's sympathetic sequence to be represented. In that case, even if the user-specified sequence is not included in the SIF, the sequence specified by the user is the probe set identifier corresponding to the SIF identifying the probe set. As those skilled in the relevant art will now understand, it is possible that the user specification requires parallelization with respect to ESTs and partial sequences of genes or ESTs.

Another example of a probe set identifier is an accession number for a gene or EST. Gene and EST accession numbers are publicly available. A probe set can thus be identified by an accession number or the number of one or more ESTs and/or genes corresponding to the probe set. Concordance between probe sets and EST's or genes can be maintained in an appropriate database, such as accessed by database application 230 or native library database 516, where the concordance can be provided to the user. Likewise, gene fragments or sequences other than ESTs can be mapped (e.g., by consulting appropriate databases) to the corresponding genes or ESTs for the purpose of using their publicly available accession numbers as probe set identifiers. . For example, a user may be interested in product or genome information related to a particular SIF derived from EST-1 and EST-2. The user may be equipped with agreement between the SIF (or part or all of the SIF sequence) and EST-1 or EST-2 or both. In order to obtain the product or genome data related to the SIF, or its partial sequence, the user can select the access number of EST-1, EST-2 or both.

Genome Net Entry 400

The GenomeNet portal 400 provides data associated with one or more genes or ESTs to a user 101 . Each gene or EST has at least one corresponding probe set identified by a probe set identifier which, as stated, may be, as an illustrative and non-limiting example, a number, name, connection Enter numbers, symbols, graphical representations (such as dots or highlighted list entries), or nucleotide sequences. This corresponding probe set can allow detection of the expression of its corresponding gene. Portal 400 provides genomic information and/or information about biological products to user 101 in response to user selection of one or more probe set identifiers. This information can assist user 101 in interpreting the results of experiments, and in designing or conducting subsequent experiments.

FIG. 5 is a functional block diagram of one of many possible embodiments of portal 400 . In this example, portal 400 has hardware components comprising three computer platforms: database server 510 , Internet server 530 , and application server 520 . The various functional units of portal 400, such as database manager 512, input and output managers 532 and 534, and user services manager 522 perform their operations on these computer platforms. That is, in a typical implementation, the functions of managers 512 , 532 , 534 and 522 are performed by the execution of software applications and by a computer platform represented by servers 510 , 530 and 520 . Portal 400 is described first with respect to its computer platform and then with respect to its functional units.

Each of servers 510, 520, and 530 may be any type of computer platform known or to be developed in the future, although they typically belong to the class of computers commonly referred to as servers. However, they can also be mainframes, workstations, or other computer types. They are connected by any known or future cable type or other communication system, both networked or not. They may be positioned relative to each other or they may actually be separate. Different operating systems may be used on any computer platform depending on the type and/or selected computer platform configuration. Suitable operating systems include Windows NT ^(R) , Sun Solaris, Linux, OS/400, Compaq Tru64, Unix, SGIIRIX, Siemens Reliant Unix, and the like.

There are significant advantages to implementing the functionality of portal 400 on multiple computer platforms in this manner, such as low cost provisioning, database conversion or conversion to enterprise applications, and/or more efficient firewalls. However, other configurations are also possible. For example, it is well known to those of ordinary skill in the relevant art that in addition to the three-tier server-side components represented by FIG. 5, so-called dual or N-tier structures are possible. See, for example, E. Roman, Mastering Enterprise JavaBeans ^™ and the Java ^™ 2 Platform (John Wiley & Sons Company, NY, 1999) and J. Schneider and R. Arora, Using EnterpriseJava ^™ (Que Company, Indianapolis 1997), for general purposes at Both of these are incorporated herein by reference in their entirety.

It is clear that many hardware and related software or program package components for Internet commerce not shown in FIG. 5 can be implemented in a server-side architecture. Not shown are components that implement one or more firewalls to protect data and applications, uninterruptible power supplies, LAN switches, web server routing software, and many others. Likewise, various computer components commonly included in server class computing platforms and other types of computers would be included but not shown. These components include, for example, processors, storage units, input/output devices, buses, and the components described above in relation to the user computer 103 . Those of ordinary skill in the art will readily understand how to implement these and other conventional components.

The functional units of the portal 400 can also be implemented according to various software providers and platforms (although some or all of the functions of the portal 400 can also be implemented by hardware or program packages). Among the various commercial products available for implementing e-commerce portals is BEA WebLogic from BEA Systems, which is a so-called "middleware" application. These and other middleware applications are sometimes referred to as "application servers", but are not to be confused with application server 520, which is a computer. The function of these middleware applications is usually to assist other software units (such as managers 512, 522 or 532) to share resources and coordinate behavior. The goals include making it easier to write, maintain, and change the software unit to avoid data blocking, and to prevent system freezes or recovery from system failures. Thus, these middleware applications can provide load balancing, failover, and fault tolerance, all of which features will be understood by those of ordinary skill in the relevant art.

Other development products, such as the Java( ^TM) 2 platform from Sun Microsystems, can be employed in portal 400 to provide a set of application programming interfaces (APIs), especially to improve implementation scalability and secure components. A platform called J2EE (Java ^(TM) 2 Enterprise Edition) from Sun Microsystems is configured for use with Enterprise JavaBeans. Enterprise JavaBeans simplifies the structure of server-side components using distributed object applications written in the Java language. Thus, in one implementation, the functional units of portal 400 may be written in Java and implemented using J2EE and Enterprise JavaBeans. As will be appreciated by those of ordinary skill in the art, various other software development methods or structures may be used to implement the functional units of portal 400 and their interconnections.

One implementation of these platforms and components is shown in FIG. 6 . Figure 6 is a simplified diagram illustrating the interaction between the client Internet client 410 on the user side and the input and output managers 532 and 534 of the Internet server 530 on the portal side, and the three layers of the portal 400 (server 510, 520, and 530). Browser 605 on client 410 sends and receives HTML documents 620 to and from server 530 . HTML document 625 includes applet 627 . Browser 605 running on user computer 103 provides a runtime container for applet 627 . Functions of managers 532 and 534 on server 530, such as GUI operations, may be implemented via servlets and/or JSP 640 along with Java ^™ platform operations. The servlet engine executing on server 530 provides a runtime container for servlet 640 . JSP (Java Server Home Page) from Sun Microsystems is a text-like environment for GUI operations, an alternative is ASP (Active Server Home Page) from Microsoft. App server 650 is a product referred to above as middleware, and executes on application server 520 . EJB (Enterprise JavaBeans ^™ ) is a standard specifying the structure for enterprise beans, which are application components. Similarly, CORBA (Common Object Request Broker Architecture) is a standard for distributed object systems, ie, the CORBA standard is implemented by CORBA in turn products such as Java ^(TM) IDL. An example of an EJB compliant product is referred to above as WebLogic. Further details of the implementation of standards, platforms, components and other elements for Internet access and its communication with clients are well known to those skilled in the relevant art.

As mentioned above, one functional unit of the portal 400 is the input manager 532 . Manager 532 receives a set, ie, one or more probe set identifiers, from user 101 via Internet 499 . Manager 532 processes and forwards these messages to subscriber service manager 522 . These functions are performed according to techniques known and common to the operation of Internet servers, which servers are also generally described with similar textual references. Another functional unit of portal 400 is output manager 534 . Also in accordance with those known methods, the manager 534 provides the information assembled by the subscriber service manager 522 to the subscriber 101 via the Internet 499, one aspect of which is described above with respect to FIG. The information assembled by manager 522 is represented in Figure 5 as data 524, labeled "Integrated Genome and/or Product Web Pages in Response to User Request". The data is inter alia in the sense that the data is integrated at least in part on the specification of identifiers set by the probes of the user 101 , thus corresponding to those identifiers the genes and/or ESTs have a shared relationship. Data 524 represented by manager 534 can be implemented in various known ways. As some examples, data 524 may include HTML or XML documents, email or other files, or other forms of data. This data may include Internet URL addresses so that user 101 may retrieve additional HTML, XML or other documents or data from remote sources.

Portal 400 further includes database manager 512 . In the illustrated embodiment, database manager 512 coordinates the storage, maintenance, replenishment, and other transfer of data from and to any local databases 511 , 513 , 514 , 516 , and 518 . Manager 512 may cooperate with an appropriate database application program, such as the Oracle 8.0.5 database management system, to perform these functions.

In some implementations, the manager 512 periodically updates the local genome database 518 . Data updates in database 518 include data associated with genes or ESTs corresponding to one or more probe sets. The probe set can be used or planned for use on any microarray product, and/or desired or planned for use in any manufacturer's or researcher's microarray product. For example, the probe set can include all probe sets artificially synthesized on the GeneChip ^(R) probe array from Affymetrix company inventory, including its Arabidopsis genome array, CYP450 array, Drosophila genome array, E. coli genome array, GenFlex ^™ Marker Array, HIV PRT Plus Array, HuGeneFL Array, Human Genome U95 Panel, HuSNP Probe Array, Murine Genome U74 Panel, P53 Probe Array, Mouse Genome U34 Panel, Mouse Neurobiology Panel U34, Mouse Toxicology U34 Array Or yeast genome S98 array. The probe set may also include those for user 101 or other artificial synthesis on conventional arrays. However, the data updated in database 518 need not be so limited. Rather, it can involve many genes or ESTs. The types of data that may be stored in database 518 are described below with respect to the operation of manager 522, which is collected directly from remote sources on a regular basis and provided locally held data in database 518 to users.

Database 516 includes data of the type referenced above with respect to database application 230, ie, data associated with its corresponding gene or EST and its identifier. Database 516 also includes SIF and other library data. From time to time, the user service manager 522 provides the database manager 512 with updated information with respect to program libraries and other data. Occasionally, such updated information will be provided by the owner or administrator of the proprietary information, although such information may also be publicly available for upload on a web site.

The information stored by manager 512 in local product database 514 may likewise be provided by vendors, distributors or agents or obtained from public sources such as web sites. A wide variety of related product information may be included in the database 514 including, for example, availability, price, composition, suitability, or ordering data. The information may relate to a wide variety of products, including all types of biological devices or substances, or all types of reagents that may be used in biological devices or substances. To name a few examples, the device, substance or reagent can be an oligonucleotide, probe array, clone, antibody or protein. Data stored in database 514 may also include links, such as Internet URL addresses, to remote locations where product data is available, such as vendor websites.

The database 511 includes information of probe set identifiers related to the sequences of the probes. This information can be provided by the manufacturer of the probe, the researcher designing the probe for use in a fixed-point array or other conventional array, or others. Furthermore, the application of the portal 400 is not limited to probes arranged in an array. As noted, the probes may be immobilized on or in beads, optical fibers, or other substrates or media. Therefore, database 511 may also include information considering these probe sequences.

Database 519 includes information about users and the accounts they use to conduct business with or through portal 400 . Any kind of account information may be obtained from the user, such as current orders, past orders, etc., all of which would be readily apparent to those of ordinary skill in the art. Meanwhile, information related to the user can be studied by recording and/or analyzing the interaction of the user with the portal 400, according to known methods used in electronic commerce. For example, user business manager 522 may note the genomic regions of user interest, their purchasing or product query behavior, their frequency of visits to various businesses, etc., and provide this information to database manager 512 for use in Stored or updated in the database 519.

Another functional unit of the portal 400 is the user service manager 522 . Manager 522 may periodically cause database manager 512 to update local genome database 518 from various sources, such as remote database 402 . For example, on any chronological schedule (e.g., daily, weekly, etc.), the manager 522 can initiate a search of the remote database 402 by formulating appropriate queries, addressing various databases, according to known methods 402, or by other conventional methods for conducting data searches and/or retrieving data or documents over the Internet. These search queries and corresponding addresses may be provided to output manager 534 for presentation to database 402 in a known manner. Input manager 532 receives replies to queries and provides them to manager 522, which in turn provides them to database manager 512 for updating database 518, all according to various known methods for managing information flow, from and within the Internet site, .

Portal application manager 526 manages the administrative aspects of portal 400, possibly with the assistance of middleware products such as application server products. One of these administrative tasks described may be issuing periodic instructions to manager 522 to initiate regular updates of database 518 . Alternatively, manager 522 may automatically initiate this task. Not all data in database 518 is updated according to the same periodic schedule. Rather, data updates are generally for different types of data and/or from different sources, according to different schedules. Furthermore, these timetables can change and do not have to follow consistent times. That is, an update for specific data may occur one day later, and then be updated again two days later, and then continue to change in different cycles. Many factors can affect the determination by manager 526 or manager 522 to maintain or vary these periods, such as response times from the various remote databases 402, the value and/or timeliness of information in those databases, and access The associated cost considerations or licensing of the database, the amount of information that must be accessed, etc.

In some implementations, the manager 522 constructs from data in the local genome database 518 a set of data associated with the set of genes or ESTs corresponding to the probe set identifier selected by the user 101 . The user selection may be forwarded by input manager 532 to manager 522 in known manner. Based on the user selections, manager 522 obtains data from database 518 by formulating appropriate queries, such as a SQL language, also according to known methods. Manager 522 then forwards the query to database manager 512 for execution against database 518 .

In this manner, various types of data can be accessed from the remote database 402 and maintained in the local genome database 518, as described. Examples include sequence data, exonic structure or location data, splice variant data, marker structure or location data, polymorphism data, homology data, protein homology data, pathway data, alternative gene name data, literature enumeration data, and Annotate data. Many other examples are possible as well. Likewise, genomic data that is not currently available but becomes available in the future can be accessed and maintained locally as described herein. Examples of remote databases 402 currently available for access as described include GenBank, GenBank New, SwissProt, GenPept, DB EST, Unigene, PIR, Prosite, PPAM, Prodom, Blocks, PDB, PDBfinder, EC Enzyme, Kegg Pathway, Kegg Ligand, OMIM, OMIM Map, OMIM Allele, DB SNP, and PubMed. Hundreds or thousands of other databases currently exist suitable, so this list is merely illustrative.

In addition, local genomic database 518 may also be supplemented with data obtained or derived (by user services manager 522 ) from other local databases served by database manager 512 . In particular, although local product database 514 is shown as separate from database 518 for ease of illustration, it may be the same database. Alternatively, all or a portion of the data in database 514 may be copied or made accessible from database 518 .

A more specific example is now provided of how the user services manager 522 receives and responds to requests from users 101, both for genomic information and for product information and/or ordering. These examples are described with respect to FIGS. 7 , 8 and 9 .

FIG. 7 is a flowchart illustrating an exemplary method by which an embodiment of a portal 400 may respond to a user request for genomic or product information. Following step 710 of this example, input manager 532 receives a request for data by user 101 from client 410 via Internet 499 . For example, the request may include an HTML or XML document that includes the user's 101 selection of a certain probe setting identifier. As stated, the probe set identifier may be a number, name, accession number, symbol, graphical representation, or nucleotide or other sequence, as a non-limiting example. In some cases, user 101 may make this selection by utilizing one or more analysis applications 199A to select a probe set identifier (e.g., draw a ring around a point as described above), and then use various known A method of activating communication with portal 400, such as a right mouse click. The request may also specify whether the user 101 is interested in genomic and/or product data and details of the type of data desired, according to various known methods. For example, the user 101 may select a category of a product, a seller or a name of a product, etc. from a drop-down menu. As mentioned above, the manager 532 provides the request of the user 101 to the user service manager 522 .

According to step 720 , the user service manager 522 initiates the identification of the user 101 . FIG. 8 is a block diagram showing in more detail the functional elements of manager 522, including account ID determiner 822, which performs the task of identifying user 101 in this illustrative embodiment. The determiner 822 may utilize any known method to obtain this information, such as using cookies technology or extracting from a user request for an identification number entered by the user. Via database manager 512 , determiner 810 may compare the user identification to an entry in user account database 513 to further identify user 101 . In another embodiment, as described above, the identity of the user 101 need not be obtained, although statistics or information related to the user's 101 request may be recorded.

According to step 725, the user services manager 522 formulates an appropriate query (eg, using a version of the SQL language) for correlating probe set identifiers with corresponding genes or ESTs. Gene or EST determiner 820 is a functional unit of manager 522 that exemplarily performs this operational task. Determiner 820 forwards the query to database manager 512 . If the probe set identifier provided by user 101 includes sequence information, the query may be sought from database 511, and/or from SIF information in database 516, identification of one or more probe sets having corresponding (e.g. , similar to the sequence of the biological meaning). If the probe set identifier includes a name or number (e.g., an access number), the query can look for an identification of the probe set from the database 516, including and name, number, and others corresponding to the gene or EST probes set identifier-related data. The user 101 can also use the database application 230 locally to obtain this information and include it in the information request according to known methods. In this case, step 725 need not be performed.

As indicated at step 730, the user services manager 522 will then correlate the indicated genes and/or ESTs with the genomic information and/or product information. The performance of this operational task is performed by correlator 830 in the illustrated example. In one of many possible embodiments, correlator 830 formulates a query via database manager 512 to database 513 to obtain links to appropriate information in local product database 514 and/or local genome database 518 . FIG. 9 is a simplified graphical representation of a database 513. Those of ordinary skill in the art will appreciate that this representation is provided for clarity of illustration and that many other embodiments are possible. In one aspect of an appropriate query to the database 513, to illustrate the assumed relational database, a gene or EST access number 902 is associated with a link 904 to a probe set ID 912. As represented in FIG. 9, multiple genes and/or ESTs can be related to the same probe set ID by associating the two IDs 902A and 902B to the same link 904N. The information used to establish this correlation is similar to that provided in database 516 as described above, and thus the link may be predetermined using database 516 or determined dynamically.

In another embodiment, the correlator 830 simply correlates one or more genetic or EST identifiers, such as accession numbers, with a product, such as a biologic. These embodiments are represented in FIG. 8 by arrows leading from determiner 810 (which is optional) to correlator 830 . The correlation can be accomplished in any variety of conventional ways, such as by providing a query to the local product database 514, to the remote home page 404 and/or the remote database 402. These queries may be indexed or keyed by category, type, name, or vendor of the product, as may be appropriate, for example, in inspection lookup tables, relational databases, or other data structures. Additionally, the query may search products, product web pages, or other sources of product data that are logically or syntactically related to the gene or EST identifier, according to methods known to those of ordinary skill in the relevant art. The results of this query may then be provided to the user 101 by the output manager 534 , such as to the client 410 via the Internet 499 .

Along with an appropriate link 904 to a probe set ID 912, one or more links 916 to related product and/or genomic data can be obtained. For example, link 904N may link to probe set 912C, which is related to link 916C to related product and/or genomic data. The information used to establish this correlation may be predetermined by the user based on expert input and/or computer-implemented analysis of the nature of the query (eg, statistically and/or by an adaptive system such as a neural network). For example, it may be observed or expected (by human or computer, as described) that a user conducting a gene expression experiment leading to the identification of a certain gene may wish to use antibodies against that gene to proceed to control protein level experiments. The relationship between genes and appropriate antibodies may be stored in a suitable database, such as database 516 . Thus link 916C may include a link to a product or genome data identifier that identifies a link to data on the appropriate antibody (e.g., a link to product/genome ID 922A), identifies a general antibody catalog link (e.g., ID922B), or Identify probe array links (eg, ID922C) explicitly designed to detect another gene of interest in the junction form. For purposes of illustration, especially in this example, assume that link 916C leads to ID 922C. Information regarding the availability of the junction variable probe array may be predetermined by the content of link 926 . For example, a link 926D (related to ID 922C as shown) to an Internet and/or database query URL leading to a vendor's web page, local product database 514 and/or local genome database 518 may be stored. Likewise, the content of link 926D may be dynamically determined by database 514 or 518 or a remote database such as database 402 or web page 404 . These and similar processes are represented by step 735 of FIG. 7 .

This illustrative arrangement of database 513 is possible for many modifications and varied embodiments, as will be appreciated by those of ordinary skill in the art. For example, probe set identification data can be linked to an array identifier, such as array ID 914 , which can then be associated with link 916 . As another of the many possible examples, a gene or EST access number could be linked directly to a product and/or genomic data ID 922, or, even directly to a link 926. An implementation such as the example provides an opportunity for the user to make wide-ranging associations based on narrower queries. For example, a user may select only one probe set identifier, but the identifier may be linked to multiple gene and/or ETS data, which may also be linked to multiple product or genomic data. In another example, link 926D may include a link to local genome database 518 . Based on probe set identifiers, gene or EST access numbers, sequence information, or other data provided or derived from user 101 queries, database 518 may retrieve relevant data according to known query and/or retrieval techniques.

Returning now to FIG. 7 , and in particular step 740 , the data returned by the query owned by correlator 830 is provided to product data processor 842 , genomic data processor 844 , or both, as appropriate returned data in nature. For ease of illustration, the functions of processors 842 and 844 are shown separately, but this is not necessary. Processors 842 and 844 apply all known presentation or data transfer techniques to prepare graphical user interfaces, files and other forms of data for transfer. The data thus processed is then provided to output manager 534 for transmission to client 410 .

In some embodiments, user 101 may respond to such data sent by expressing a desire to purchase a product or receive further information. Requests for further information may be handled in a manner similar to that described above for FIG. 7 . If the user 101 expresses a desire to purchase a product (see decision unit 745), the indicated product can be prepared for shipment or otherwise processed, and the user's account can be adjusted according to known methods for implementing electronic commerce. As one of many alternative embodiments, the customer service manager 522 can notify the product seller of the customer's 101 order, and the seller can ship or order the product to be shipped. In one aspect of this embodiment, the manager 522 will then state that the fee should be charged from the seller for the referral.

In some embodiments of portal 400, user 101 may provide portal 400 (eg, via client 410, Internet 499, and input manager 532) one or more genetic or EST ascending numbers or other genetic or EST identifiers. Alternatively, or in addition, user 101 may provide portal 400 with one or more probe set identifiers. The user 101 may obtain a probe array from a public source, from a marker that the user 101 has performed as a result of testing the probe array, or from a set of genes or ESTs that have corresponding probes on the probe array, or from any other source or in any other manner. Gene, EST and/or probe set identifiers are obtained in the same way. Input manager 532 receives one or more gene, EST or probe set identifiers and provides it or them to user services manager 522 , which formulates a query to database manager 512 . The query seeks information from a local product database 514 of product information associated with gene, EST and/or probe set identifiers, following known query methods and formats. To this end, the local product database 514 may index or find products based on or keying on any one or more gene, EST and/or probe set identifiers. Certain embodiments may include similarity matching to gene, EST, or probe set identifiers, according to known methods, for example, if all or part of the gene, EST, SFI (corresponding to the probe set identifier) sequence is submitted . Also, name concatenation functions can be implemented according to known methods such as table lookups so that alternative names or forms of gene, EST or probe set identifiers can be found and used in product data queries. Additionally, in some embodiments, manager 522 may initiate remote data retrieval of remote database 402 and/or remote vendor web page 404 to obtain product information from remote sources, in accordance with known Internet search techniques. These searches may be based on, for example, product categories associated with products, categories in the local product database 514 or sellers associated with genes, ESTs, or probe set identifiers provided by the user 101 , or sellers. Manager 522 can provide product data corresponding to gene, EST and/or probe set identifiers, obtain product data from local product database 514 and/or remote pages or databases 404 or 402, and export these via output manager 534 Product data is provided to the user 101 . For example, this product data may be included in web page 524 . In some embodiments, portal 400 provides a system for providing product data, typically biologics data. The system comprises: an input manager 532, which receives one or more gene, EST, and/or probe set identifiers from a user 101; a user services manager 522, which correlates a gene, EST, and/or probe set identifier with one or more product data; , and/or probe set identifiers, and make (e.g., via the database manager 512) product data either obtain from the home page 404 or the database 402, such as from the local database 514 or, in some embodiments, remotely from the home page 404 or the database 402; Manager 534, which provides the product data to the user 101.

Similarly, a method of providing biological product data is provided, the method comprising the steps of: receiving from a user 101 one or more gene, EST, and/or probe set identifiers; EST, and/or probe set identifier; having product data obtained locally (eg, database 514 ) or remotely (eg, home page 404 or database 402 ); and providing the product data to user 101 .

As noted above, the functional units of portal 400 may be implemented in hardware, software, program packages, or any combination thereof. In the embodiments described above, it is generally assumed that the functions of the portal 400 are implemented in software for the sake of convenience. That is, the functional units of the illustrated embodiments comprise software instruction means to perform the described functions. These software instructions can be programmed in any programming language, such as Java, Perl, C++, other high-level programming languages, low-level languages, and any combination thereof. The functional units of portal 400 may thus be referred to as executing “a set of GenomeNet portal instructions” and their functional units may similarly be described as means of GenomeNet portal instructions executed by servers 510 , 520 , and 530 .

In some embodiments, a computer program product is described as comprising a computer-usable medium having control logic (computer software program, including program code) stored thereon. When executed by a processor, the control logic causes the processor to implement the functions of portal 400 described herein. In another embodiment, for example, some of the functions described above are implemented primarily in hardware using a hardware state machine. Implementation of a hardware state machine such that implementing the functions described herein will be apparent to those skilled in the relevant arts.

Having described various embodiments and implementations, it should be apparent to those skilled in the relevant arts that the foregoing embodiments have been presented by way of illustration only, and not limitation. Many other schemes are possible for distributing functionality among the various functional units of the illustrated embodiments. The functionality of any unit may be performed in various ways in alternative embodiments. Likewise, the functions of several units may be performed by fewer or a single unit in alternative embodiments.

For example, for clarity, the functionality of the user service manager 522 is described as being implemented by the functional units shown in FIG. 8 . However, manager 522 need not necessarily be divided into these or other distinct functional units. Similarly, operations of specific functional units that are described separately for convenience do not necessarily need to be performed separately. For example, some or all of the functions of product data processor 842 may be performed by genomic data processor 844, and vice versa. Similarly, in some embodiments all functional units may perform fewer or different operations than those described with respect to the illustrated embodiments. Also, in a particular embodiment, shown functional units may be incorporated within other functional units for clarity of illustration.

For example, the functionality of processors 842 and 844 may be grouped into a single functional unit. Similarly, some or all of the functions of database manager 512 may be performed by user services manager 522 and/or by input manager 532 .

Also, the sequence of functions or parts of functions may often vary. For example, the functions of account ID determiner 810 may be performed after user data processor 840 . Thus the data flow and control in Figure 8 is merely exemplary in this regard. Similarly, the method steps shown in Figure 7 are not necessarily always performed in the order suggested by the illustrative examples of those Figures. For example, method step 720 of identifying a user may be performed after step 725 , 730 or 735 .

Certain functional units, files, data structures, etc. may be represented in the illustrated embodiment as being located in the system memory 120 of the computer 100 or typically in the server 510 , 520 , or 530 . However, in other embodiments, they may be located or distributed on computer systems or other platforms that are located and/or remote from each other. For example, one or more data files or data structures 511, 513, 514, 516 or 518 shown in FIG. In these cases, the operation of database manager 512 with respect to these data files or data structures may be performed over a network or by any of numerous other known means for transferring data and/or control to or from remote locations. .

Furthermore, those skilled in the relevant art will appreciate that the control and data flow between and among the functional units and the various data structures may be varied in many ways from that described above. In particular, intermediate functional units (not shown) may directly control data flow, and the functions of the various units may be combined, decomposed or reordered to allow parallel processing or for other reasons. Likewise, intermediate data structures or files may be used, and various described data structures or files may be combined or permuted. Accordingly, many other embodiments and modifications thereof are within the scope of the invention as defined by the appended claims and their equivalents.

Claims (43)

1. A system for providing data about one or more genes or expressed sequence tags, wherein each gene or expressed sequence tag has at least one corresponding probe set identified by a probe set identifier and is capable of detecting Biomolecules, including: constituting an input manager and configured to receive a selection from a user of a first set of one or more probe setting identifiers; constituting a gene caller configured to identify a first set of one or more genes or expressed sequence tags corresponding to the probe set identified by the first set of probe set identifiers; constituting a correlator configured to correlate the first set of gene or expressed sequence tags with the first set of one or more data; and Constitutes the output manager and is set to provide the first set of data to the user. 2. The system of claim 1, wherein: The first set of probe set identifiers identifies a set of probe sets capable of detecting biomolecules including nucleic acids. 3. The system of claim 1, wherein: The first set of probe set identifiers identifies a set of probe sets capable of detecting biomolecules comprising mRNA transcripts of corresponding genes. 4. The system of claim 1, wherein: The first set of probe set identifiers includes probe set identifiers of the second set of one or more probe set identifiers that have been able to detect all or part of the expression or differential of their corresponding gene or expressed sequence tags. 5. The system of claim 4, wherein: The probe set groups identified by the second set of probe set identifiers are positioned on the one or more probe arrays. 6. The system of claim 5, wherein: The probe set identified by the second set of probe set identifiers includes in situ synthesized oligonucleotides. 7. The system of claim 6, wherein: The probe array includes a probe array comprising oligonucleotide probes. 8. The system of claim 5, wherein: At least one probe set group identified by the second set of probe set identifiers consists of a single point on the point-shaped probe array. 9. The system of claim 5, wherein: The probe array includes a dot array. 10. The system of claim 9, wherein: At least one spot of the spot array comprises an oligonucleotide. 11. The system of claim 1, wherein: said users include remote users, and The input manager receives selections from remote users over the network. 12. The system of claim 11, wherein: The network includes the Internet. 13. The system of claim 1, wherein: At least a first probe set identifier of the first set of probe set identifiers includes a gene identifier for a gene corresponding to the first probe set identifier. 14. The system of claim 13, wherein: Gene identifiers include an accession number. 15. The system of claim 1, wherein: A user selects a first set of probe set identifiers based at least in part on an indication of a level of expression or differential expression of a gene or expressed sequence tag corresponding to an expression identified by the first set of probe set identifiers. group of probe settings. 16. The system of claim 1, wherein: The first set of one or more data includes one or any combination of product data regarding availability, price, composition, suitability, or order. 17. The system of claim 16, wherein: The first set of one or more data includes product data about the biological device or material, or reagents that may be used with a biological device or material. 18. The system of claim 17, wherein: Devices, materials, or reagents include one or any combination of oligonucleotides, probe arrays, nucleotide clones, antibodies, or proteins. 19. The system of claim 1, wherein: The first set of one or more data includes at least in part data stored in the local product database. 20. The system of claim 19, wherein: The first set of one or more data includes at least one link to remote data representing a seller of the biological product. 21. A system for providing product data on one or more genes or expressed sequence tags comprising: constitutes an input manager and is configured to receive one or more gene or expressed sequence tag identifiers; constituting a correlator and configured to correlate the gene or expressed sequence tag identifier with one or more product data; and Constitutes the output manager and is set up to provide product data to the user. 22. The system of claim 21, wherein: said product data is biological product data. 23. The system of claim 21, wherein: The gene or expressed sequence tag identifier includes a gene or expressed sequence tag access number. 24. A method for providing data about one or more genes or expressed sequence tags, wherein each gene or expressed sequence tag has at least a corresponding probe set identified by a probe set identifier, and is capable of detecting a A biomolecule comprising the steps of: the input manager receives a selection of a first set of one or more probe setting identifiers from the user; the gene determiner identifies one or more genes or expressed sequence tags corresponding to a first set of probe sets identified by the first set of probe set identifiers; a correlator correlating the first set of one or more data with the first set of gene or expressed sequence tags; and The output manager provides the first set of data to the user. 25. The method of claim 24, wherein The first set of probe set identifiers identifies a set of probe sets capable of detecting biomolecules including nucleic acids. 26. The method of claim 24, wherein: The first set of probe set identifiers identifies a set of probe sets capable of detecting biomolecules comprising mRNA transcripts of corresponding genes. 27. A method for providing product data about one or more genes or expressed sequence tags, the product data being provided by a system comprising an input manager, a correlator and an output manager, the method comprising: receiving, by an input manager, one or more gene or expressed sequence tag identifiers; correlating the one or more product data with gene or expressed sequence tag identifiers by a correlator; and The output manager provides product data to the user. 28. The method of claim 27, adapted to process requests or commands received from users over a network. 29. The method of claim 28, comprising identifying a first set of one or more gene or expressed sequence tags corresponding to probe set identifiers capable of detecting biomolecules. 30. The method of claim 29, wherein the user selects a first set of one or more probe setting identifiers, and the first set of product data is provided to the user via the one or more web pages. 31. The method of claim 30, wherein: In the first group, the probe set identifier identifies a probe set capable of detecting biomolecules including nucleic acids. 32. The method of claim 30, wherein: In the first set, the probe set identifier identifies the set of probe sets capable of detecting biomolecules comprising mRNA transcripts of the corresponding gene. 33. The method of claim 30, further comprising the step of: A second user selection of one or more products to purchase is received over the network based on the portion of the first set of product data provided to the user. 34. The method of claim 33, further comprising the step of: identify an account corresponding to the user, and An account corresponding to the user is adjusted based at least in part on price data corresponding to the product selected by the second user. 35. The method of claim 33, further comprising the step of: The product is sold to the user based on the second user's selection of the product. 36. The method of claim 30, wherein a user performs at least one gene expression experiment on an array of probes to select said probe set identifier. 37. The method of claim 30, wherein the user selects the first set of probe set identifiers based on an indication of the extent of expression of genes or expressed sequence tags corresponding to the probe sets identified by the first set of probe set identifiers. 38. The method of claim 30, wherein: At least one probe set identified by the first set of probe set identifiers is disposed on the one or more probe arrays. 39. The method of claim 30, wherein: Said product data is selected from the group comprising product data about availability, composition, suitability and order. 40. The method of claim 30, wherein: The product data is selected from the group comprising product data pertaining to the biological device or material, or a reagent that may be used in the biological device or material. 41. The method of claim 30, wherein: The product data is selected from the group consisting of product data related to oligonucleotides, probe arrays, nucleotide clones, antibodies, or proteins. 42. The method of claim 30, wherein: This product data is associated with PCR primers and/or PCR probes. 43. The method of claim 30, wherein the product data includes at least one link to remote data representing a seller of the biological product.

Images