Claims
- 1. A system for providing data related to one or more genes or EST's, wherein each gene or EST has at least one corresponding probe set identified by a probe-set identifier and capable of enabling detection of a biological molecule, comprising:
an input manager constructed and arranged to receive from a user a selection of a first set of one or more of the probe-set identifiers; a gene determiner constructed and arranged to identify a first set of one or more genes or EST's corresponding to the probe sets identified by the first set of probe-set identifiers; a correlator constructed and arranged to correlate the first set of genes or EST's with a first set of one or more data; and an output manager constructed and arranged to provide the first set of data to the user.
- 2. The system of claim 1, wherein:
the first set of probe-set identifiers identify probe sets that are capable of enabling the detection of a biological molecule that consists of nucleic acid.
- 3. The system of claim 1, wherein:
the first set of probe-set identifiers identify probe sets that are capable of enabling the detection of a biological molecule that consists of mRNA transcripts of corresponding genes.
- 4. The system of claim 1, wherein:
the first set of probe-set identifiers comprises all or part of a second set of one or more probe-set identifiers of probe sets that have enabled detection of the expression or differential expression of their corresponding genes or EST's.
- 5. The system of claim 4, wherein:
the probe sets identified by the second set of probe-set identifiers are disposed on one or more probe arrays.
- 6. The system of claim 5, wherein:
the probe sets identified by the second set of probe-set identifiers include in situ synthesized oligonucleotides.
- 7. The system of claim 6, wherein:
the probe arrays include a GeneChip® probe array.
- 8. The system of claim 5, wherein:
at least one of the probe sets identified by the second set of probe-set identifiers consists of a single spot on a spotted probe array.
- 9. The system of claim 5, wherein:
the probe arrays include a spotted array.
- 10. The system of claim 9, wherein:
at least one spot of the spotted array comprises an oligonucleotide.
- 11. The system of claim 1, wherein:
the user includes a remote user, and the input manager receives the remote user's selection over a 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 comprises a gene identifier of the gene corresponding to the first probe-set identifier.
- 14. The system of claim 13, wherein:
the gene identifier comprises an accession number.
- 15. The system of claim 1, wherein:
the user selects the first set of probe-set identifiers based, at least in part, on an indication of a degree of expression or differential expression of the genes or EST's corresponding to the probe sets identified by the first set of probe-set identifiers.
- 16. The system of claim 1, wherein:
the first set of one or more data includes one or any combination of product data related to availability, pricing, composition, suitability, or ordering.
- 17. The system of claim 16, wherein:
the first set of one or more data includes product data regarding a biological device or substance, or a reagent that may be used with a biological device or substance.
- 18. The system of claim 17, wherein:
the device, substance, or reagent includes one or any combination of an oligonucleotide, probe array, clone, antibody, or protein.
- 19. The system of claim 1, wherein:
the first set of one or more data includes data stored, at least in part, in a local products 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 vendor of biological products.
- 21. The system of claim 20, wherein:
the link includes an Internet URL.
- 22. The system of claim 20, wherein:
the remote data include an HTML or XML document.
- 23. The system of claim 1, wherein:
the user includes a remote user, and the output manager provides the first set of product data to the user over a network.
- 24. The system of claim 23, wherein:
the network includes the Internet.
- 25. A method for providing data related to one or more genes or EST's, wherein each gene or EST has at least one corresponding probe set identified by a probe-set identifier and capable of enabling detection of a biological molecule, comprising the steps of:
receiving from a user a selection of a first set of one or more of the probe-set identifiers; identifying a first set of one or more genes or EST's corresponding to the probe sets identified by the first set of probe-set identifiers; correlating the first set of genes or EST's with a first set of one or more data; and providing the first set of data to the user.
- 26. The method of claim 25, wherein:
the first set of probe-set identifiers identify probe sets that are capable of enabling the detection of a biological molecule that consists of nucleic acid.
- 27. The method of claim 25, wherein:
the first set of probe-set identifiers identify probe sets that are capable of enabling the detection of a biological molecule that consists of mRNA transcripts of corresponding genes.
- 28. A computer program product for providing data related to one or more genes or EST's, wherein each gene or EST has at least one corresponding probe set identified by a probe-set identifier and capable of enabling detection of a biological molecule, wherein the computer program product, when executed on a computer system, performs a method comprising the steps of:
receiving from a user a selection of a first set of one or more of the probe-set identifiers; identifying a first set of one or more genes or EST's corresponding to the probe sets identified by the first set of probe-set identifiers; correlating the first set of genes or EST's with a first set of one or more data; and providing the first set of data to the user.
- 29. The computer program product of claim 28, wherein:
the first set of probe-set identifiers identify probe sets that are capable of enabling the detection of a biological molecule that consists of nucleic acid.
- 30. The computer program product of claim 28, wherein:
the first set of probe-set identifiers identify probe sets that are capable of enabling the detection of a biological molecule that consists of mRNA transcripts of corresponding genes.
- 31. A system for providing data related to one or more genes or EST's, wherein each gene or EST has at least one corresponding probe set identified by a probe-set identifier and capable of enabling detection of a biological molecule, comprising:
an input manager constructed and arranged to receive over the Internet from a user a selection of a first set of one or more of the probe-set identifiers comprising all or part of a second set of one or more probe-set identifiers of probe sets that have enabled detection of the expression or differential expression of their corresponding genes or EST's; a gene determiner constructed and arranged to identify a first set of one or more genes or EST's corresponding to the probe sets identified by the first set of probe-set identifiers; a correlator constructed and arranged to correlate the first set of genes or EST's with a first set of one or more product data regarding a biological device or substance, or a reagent that may be used with a biological device or substance; and an output manager constructed and arranged to provide the first set of product data to the user.
- 32. The system of claim 31, wherein:
the first set of probe-set identifiers identify probe sets that are capable of enabling the detection of a biological molecule that consists of nucleic acid.
- 33. The system of claim 31, wherein:
the first set of probe-set identifiers identify probe sets that are capable of enabling the detection of a biological molecule that consists of mRNA transcripts of corresponding genes.
- 34. The system of claim 31, wherein:
at least one of the probe sets identified by the first set of probe-set identifiers is disposed on a GeneChip® probe array.
- 35. A system for providing data related to one or more genes or EST's, wherein each gene or EST has at least one corresponding probe set identified by a probe-set identifier and capable of enabling detection of a biological molecule, comprising:
an input manager constructed and arranged to receive from a user a selection of a first set of one or more of the probe-set identifiers; a gene determiner constructed and arranged to identify a first set of one or more genes or EST's corresponding to the probe sets identified by the first set of probe-set identifiers; an account identification determiner constructed and arranged to identify an account corresponding to the user; a correlator constructed and arranged to correlate the first set of genes or EST's with a first set of one or more product data including product pricing data; an account data processor constructed and arranged to adjust the account corresponding to the user based, at least in part, on the product pricing data; and an output manager constructed and arranged to provide the first set of product data to the user.
- 36. The system of claim 35, wherein:
the first set of probe-set identifiers identify probe sets that are capable of enabling the detection of a biological molecule that consists of nucleic acid.
- 37. The system of claim 35, wherein:
the first set of probe-set identifiers identify probe sets that are capable of enabling the detection of a biological molecule that consists of mRNA transcripts of corresponding genes.
- 38. The system of claim 35, wherein:
at least one of the probe sets identified by the first set of probe-set identifiers is disposed on a GeneChip® probe array.
- 39. A system for processing an order by a user to purchase one or more products, comprising:
an input manager constructed and arranged to receive from a user over the Internet a first user selection of a first set of one or more probe-set identifiers, wherein each probe-set identifier identifies a probe set capable of enabling detection of a biological molecule; a gene determiner constructed and arranged to identify a first set of one or more genes or EST's corresponding to the probe sets identified by the first set of probe-set identifiers; an account identification determiner constructed and arranged to identify an account corresponding to the user; a gene-to-order correlator constructed and arranged to correlate the first set of genes or EST's with a first set of one or more product data including product pricing data; and an output manager constructed and arranged to provide at least a portion of the first set of product data to the user.
- 40. The system of claim 39, wherein:
the first set of probe-set identifiers identify probe sets that are capable of enabling the detection of a biological molecule that consists of nucleic acid.
- 41. The system of claim 39, wherein:
the first set of probe-set identifiers identify probe sets that are capable of enabling the detection of a biological molecule that consists of mRNA transcripts of corresponding genes.
- 42. The system of claim 39, wherein:
the input manager further is constructed and arranged to receive from the user a second user selection of one or more products for purchase based on the first set of product data.
- 43. The system of claim 42, further comprising:
an account data processor constructed and arranged to adjust the account corresponding to the user based, at least in part, on the product pricing data corresponding to the second user selection.
- 44. A method for processing an inquiry or order by a user regarding one or more products, comprising the steps of:
receiving from a user a selection of a first set of one or more probe-set identifiers, wherein each probe-set identifier identifies a probe set capable of enabling detection of a biological molecule; identifying a first set of one or more genes or EST's corresponding to the probe sets identified by the first set of probe-set identifiers; correlating the first set of genes or EST's with a first set of one or more product data including product pricing data; and providing at least a portion of the first set of product data to the user.
- 45. The method of claim 44, wherein:
the first set of probe-set identifiers identify probe sets that are capable of enabling the detection of a biological molecule that consists of nucleic acid.
- 46. The method of claim 44, wherein:
the first set of probe-set identifiers identify probe sets that are capable of enabling the detection of a biological molecule that consists of mRNA transcripts of corresponding genes.
- 47. The method of claim 44, further comprising the step of:
receiving a second user selection of one or more products for purchase based on the portion of the first set of product data provided to the user.
- 48. The method of claim 47, further comprising the steps of:
identifying an account corresponding to the user; and adjusting the account corresponding to the user based, at least in part, on the product pricing data corresponding to the second user selection.
- 49. A method for placing a computer-implemented inquiry or order regarding purchase of one or more products, comprising the steps of:
receiving at a user computer a first user selection of a first set of one or more probe-set identifiers, wherein each probe-set identifier identifies a probe set that has enabled detection of a biological molecule; providing the first user selection over the Internet to a portal system capable of correlating product data with one or more genes or EST's corresponding to the probe sets identified by the first set of probe-set identifiers; and receiving the correlated product data from the portal system.
- 50. The method of claim 49, wherein:
the first set of probe-set identifiers identify probe sets that are capable of enabling the detection of a biological molecule that consists of nucleic acid.
- 51. The method of claim 49, wherein:
the first set of probe-set identifiers identify probe sets that are capable of enabling the detection of a biological molecule that consists of mRNA transcripts of corresponding genes.
- 52. The method of claim 49, further comprising the steps of:
enabling a second user selection of one or more of the correlated product data for purchase; and providing the second user selection to the portal system.
- 53. A system for providing data related to one or more genes or EST's, wherein each gene or EST has at least one corresponding probe set identified by a probe-set identifier and capable of enabling detection of a biological molecule, comprising:
a database manager constructed and arranged to periodically update a local genomic database comprising data related to the genes or EST's; an input manager constructed and arranged to receive from a user a selection of a first set of one or more of the probe-set identifiers; a user-service manager constructed and arranged to construct from the local genomic database a first set of data related to genes or EST's corresponding to the first set of probe-set identifiers; and an output manager constructed and arranged to provide the first set of data to the user.
- 54. The system of claim 53, wherein:
the first set of probe-set identifiers identify probe sets that are capable of enabling the detection of a biological molecule that consists of nucleic acid.
- 55. The system of claim 53, wherein:
the first set of probe-set identifiers identify probe sets that are capable of enabling the detection of a biological molecule that consists of mRNA transcripts of corresponding genes.
- 56. The system of claim 53, wherein:
the database manager updates the local genomic database according to a chronological period.
- 57. The system of claim 56, wherein:
the chronological period is predetermined.
- 58. The system of claim 56, wherein:
the chronological period is greater than about ten hours and less than about ten days.
- 59. The system of claim 53, wherein:
the database manager periodically updates the local genomic database with update data consisting of any combination of one or more of sequence data, exonic structure or location data, splice-variants data, marker structure or location data, polymorphism data, homology data, protein-family classification data, pathway data, alternative-gene naming data, literature-recitation data, or annotation data.
- 60. The system of claim 53, wherein:
the database manager periodically updates the local genomic database with update data from one or more remote databases.
- 61. The system of claim 60, wherein:
the updating from one or more remote databases comprises updating over the Internet.
- 62. The system of claim 61, wherein:
the remote databases consist of any combination of one or more of GenBank, GenBank New, SwissProt, 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 PubMed.
- 63. The system of claim 53, wherein:
the input manager is constructed and arranged to dynamically receive the user-initiated selection.
- 64. The system of claim 53, wherein:
the first group comprises all or part of a second set of one or more probe-set identifiers of probe sets that have enabled detection of the expression or differential expression of their corresponding genes or EST'S.
- 65. The system of claim 64, wherein:
the probe sets identified by the second set of probe-set identifiers are disposed on one or more probe arrays.
- 66. The system of claim 65, wherein:
the probe arrays include a GeneChip® probe array.
- 67. The system of claim 65, wherein:
the probe sets include a single spotted probe; the probe-set identifiers include a spotted probe identifier that identifies the single spotted probe; and the probe arrays include a spotted array that includes the single spotted probe.
- 68. The system of claim 67, wherein:
the single spotted probe includes an oligonucleotide.
- 69. The system of claim 64, wherein:
the user includes a remote user, and the input manager receives the remote user's selection over a network.
- 70. The system of claim 69, wherein:
the network includes the Internet.
- 71. The system of claim 53, wherein:
the user includes a remote user, and the output manager provides the first set of data to the user over a network.
- 72. The system of claim 71, wherein:
the network includes the Internet.
- 73. The system of claim 53, wherein:
at least one of the probe-set identifiers comprises a gene identifier of the gene corresponding to the probe-set identifier.
- 74. The system of claim 73, wherein:
the gene identifier comprises an accession number.
- 75. A system for providing data related to one or more genes or EST's, wherein each gene or EST has a corresponding probe set identified by a probe-set identifier and capable of enabling detection of the expression of the gene, the system comprising:
a database manager constructed and arranged to periodically update a local genomic database comprising data related to the genes or EST's, wherein the updating is done according to a predetermined period; an input manager constructed and arranged to dynamically receive a user-initiated selection of a first set of one or more of the probe-set identifiers; a user-service manager constructed and arranged to construct from the local genomic database a first set of data related to genes or EST's corresponding to the first set of probe-set identifiers; and an output manager constructed and arranged to provide the first set of data to the user.
- 76. A system for providing data related to one or more predetermined genes, or EST's, wherein each predetermined gene has a corresponding predetermined probe set uniquely identified by a probe-set identifier and capable of enabling detection of the expression of the gene, the system comprising:
a database manager constructed and arranged to periodically update a local genomic database comprising data related to the predetermined genes or EST's, wherein the updating is done according to a predetermined period; an input manager constructed and arranged to dynamically receive a user-initiated selection of a first set of one or more of the predetermined probe-set identifiers; a user-service manager constructed and arranged to construct from the local genomic database a first set of data related to genes or EST's corresponding to the first set of predetermined probe-set identifiers; and an output manager constructed and arranged to provide the first set of data to the user.
- 77. A system for providing data related to one or more genes or EST's, wherein each gene or EST has a corresponding probe set identified by a probe-set identifier and capable of enabling detection of the expression of the gene, the system comprising:
a database manager constructed and arranged to update a local genomic database comprising data related to the genes or EST's with update data from one or more remote databases, wherein the updating is done over the Internet according to a predetermined period; an input manager constructed and arranged to dynamically receive a user-initiated selection of a first set of one or more of the probe-set identifiers; a user-service manager constructed and arranged to construct from the local genomic database a first set of data related to genes or-EST's corresponding to the first set of probe-set identifiers; an output manager constructed and arranged to provide the first set of data to the user.
- 78. A system for providing data related to one or more genes or EST's, wherein each gene or EST has a corresponding probe set identified by a probe-set identifier and capable of enabling detection of the expression of the gene, the system comprising:
a database manager constructed and arranged to update a local genomic database comprising data related to the genes or EST's with update data from one or more remote databases, wherein the updating is done over the Internet according to a predetermined period; an input manager constructed and arranged to dynamically receive over the Internet a user-initiated selection of a first set of one or more of the probe-set identifiers; a user-service manager constructed and arranged to construct from the local genomic database a first set of data related to genes or EST's corresponding to the first set of probe-set identifiers; and an output manager constructed and arranged to provide over the Internet the first set of data to the user.
- 79. A method for providing data related to one or more genes or EST's, wherein each gene or EST has at least one corresponding probe set identified by a probe-set identifier and capable of enabling detection of the expression of its corresponding gene, comprising the steps of:
periodically updating a local genomic database comprising data related to the genes or EST's; receiving from a user a selection of a first set of one or more of the probe-set identifiers; constructing from the local genomic database a first set of data related to genes or EST's corresponding to the first set of probe-set identifiers; and providing the first set of data to the user.
- 80. The method of claim 79, wherein:
the local genomic database is periodically updated over the Internet from one or more remote databases with update data consisting of any combination of one or more of sequence data, exonic structure or location data, splice-variants data, marker structure or location data, polymorphism data, homology data, protein-family classification data, pathway data, alternative-gene naming data, literature-recitation data, or annotation data.
- 81. A computer program product for providing data related to one or more genes or EST's, wherein each gene or EST has at least one corresponding probe set identified by a probe-set identifier and capable of enabling detection of the expression of its corresponding gene, wherein the computer program product, when executed on a computer system, performs a method comprising the steps of:
periodically updating a local genomic database comprising data related to the genes or EST's; receiving from a user a selection of a first set of one or more of the probe-set identifiers; constructing from the local genomic database a first set of data related to genes or EST's corresponding to the first set of probe-set identifiers; and providing the first set of data to the user.
- 82. A system for providing product data related to one or more genes or EST's, wherein each gene or EST has at least one corresponding probe set identified by a probe-set identifier and capable of enabling detection of a biological molecule, comprising:
an input manager constructed and arranged to receive from a user a selection of a first set of one or more of the probe-set identifiers; a correlator constructed and arranged to correlate the first set of probe-set identifiers with a first set of one or more product data; and an output manager constructed and arranged to provide the first set of data to the user.
- 83. The system of claim 82, wherein:
the first set of probe-set identifiers identify probe sets that are capable of enabling the detection of a biological molecule that consists of nucleic acid.
- 84. The system of claim 84, wherein:
the first set of probe-set identifiers identify probe sets that are capable of enabling the detection of a biological molecule that consists of mRNA transcripts of corresponding genes.
- 85. The system of claim 84, wherein:
the probe sets identified by the second set of probe-set identifiers are disposed on one or more probe arrays.
- 86. The system of claim 85, wherein:
the user includes a remote user, and the input manager receives the remote user's selection over the Internet.
- 87. The system of claim 82, wherein:
at least a first probe-set identifier of the first set of probe-set identifiers comprises a gene identifier of the gene corresponding to the first probe-set identifier.
- 88. The system of claim 87, wherein:
the gene identifier comprises an accession number.
- 89. The system of claim 82, wherein:
the first set of one or more product data includes one or any combination of product data related to availability, pricing, composition, suitability, or ordering.
- 90. The system of claim 89, wherein:
the first set of one or more product data includes product data regarding a biological device or substance, or a reagent that may be used with a biological device or substance.
- 91. The system of claim 90, wherein:
the device, substance, or reagent includes one or any combination of an oligonucleotide, probe array, clone, antibody, or protein.
- 92. The system of claim 82, wherein:
the first set of one or more product data includes data stored, at least in part, in a local products database.
- 93. The system of claim 82, wherein:
the first set of one or more data includes at least one link to remote data representing a vendor of biological products.
- 94. A method for providing product data related to one or more genes or EST's, wherein each gene or EST has at least one corresponding probe set identified by a probe-set identifier and capable of enabling detection of a biological molecule, comprising the steps of:
receiving from a user a selection of a first set of one or more of the probe-set identifiers; correlating the first set of probe-set identifiers with a first set of one or more product data; and providing the first set of data to the user.
- 95. The method of claim 94, wherein:
the first set of probe-set identifiers identify probe sets that are capable of enabling the detection of a biological molecule that consists of nucleic acid.
- 96. The method of claim 94, wherein:
the first set of probe-set identifiers identify probe sets that are capable of enabling the detection of a biological molecule that consists of mRNA transcripts of corresponding genes.
- 97. The method of claim 94, wherein:
the probe sets identified by the first set of probe-set identifiers are disposed on one or more probe arrays.
- 98. A computer program product for providing product data related to one or more genes or EST's, wherein each gene or EST has at least one corresponding probe set identified by a probe-set identifier and capable of enabling detection of a biological molecule, wherein the computer program product, when executed on a computer system, performs a method comprising the steps of:
receiving from a user a selection of a first set of one or more of the probe-set identifiers; correlating the first set of probe-set identifiers with a first set of one or more product data; and providing the first set of data to the user.
- 99. A system for providing product data related to one or more genes or EST's, comprising:
an input manager constructed and arranged to receive one or more gene or EST identifiers over the Internet; a correlator constructed and arranged to correlate the gene or EST identifiers with one or more product data; and an output manager constructed and arranged to provide the product data to the user.
- 100. The system of claim 99, wherein:
the product data is biological product data.
- 101. The system of claim 99, wherein:
the gene or EST identifiers include a gene or EST accession number.
- 102. A method for providing product data related to one or more genes or EST's, comprising:
receiving one or more gene or EST identifiers over the Internet; correlating the gene or EST identifiers with one or more product data; and providing the product data to the user.
RELATED APPLICATION
[0001] The present application claims priority from U.S. Provisional Patent Application Serial No. 60/178,077, entitled “METHOD, SYSTEM, AND COMPUTER SOFTWARE FOR PROVIDING A GENOMIC WEB PORTAL,” filed Jan. 25, 2000, incorporated herein by reference in its entirety for all purposes.
Provisional Applications (1)
|
Number |
Date |
Country |
|
60178077 |
Jan 2000 |
US |
Continuations (1)
|
Number |
Date |
Country |
Parent |
PCT/US01/02316 |
Jan 2001 |
US |
Child |
10197621 |
Jul 2002 |
US |