Reaping the Benefits of Genomic and Proteomic Research: Intellectual Property Rights, Innovation, and Public Health (2006)

The following search algorithm is used by the Georgetown University research team to identify DNA-based U.S. patents. The search is in the patent “claims” field.

((047???* OR 119* OR 260???* OR 426* OR 435* OR 514* OR 536022* OR 5360231 OR 536024* OR 536025* OR 800*) <in> NC) AND ((“antisense” OR <case><wildcard>cDNA* OR centromere OR deoxyoligonucleotide OR deoxyribonucleic OR deoxyribonucleotide OR <case><wildcard>DNA* OR exon OR “gene” OR “genes” OR genetic OR genome OR genomic OR genotype OR haplotype OR intron OR <case><wildcard>mtDNA* OR nucleic OR nucleotide OR oligonucleotide OR oligodeoxynucleotide OR oligoribonucleotide OR plasmid OR polymorphism OR polynucleotide OR polyribonucleotide OR ribonucleotide OR ribonucleic OR “recombinant DNA” OR <case><wildcard>RNA* OR <case><wildcard>mRNA* OR <case><wildcard>rRNA* OR <case><wildcard>siRNA* OR <case><wildcard>snRNA* OR <case><wildcard>tRNA* OR ribonucleoprotein OR <case><wildcard>hnRNP* OR <case><wildcard>snRNP* OR <case><wildcard>SNP*) <in> CLAIMS))

The following search algorithms were used by Academies staff to identify U.S. patents in several genomic and proteomic categories, molecular pathways, and research tools. In all but one case the patent “claims” field was searched. The NF-kB pathway was searched in the “keyword” field because it includes an assignee restriction in the Boolean string:

1. Genes and gene regulatory sequences: (“nucleic acid” OR nucleotide OR “nucleotide sequence” OR oligonucleotide OR deoxyribonucleic OR deoxyribonucleotide OR oligoribonucleotide OR ribonucleotide OR “recombinant DNA” OR cDNA OR plasmid OR gene OR genomic) AND (“promoter” OR “enhancer” OR “response element” OR “DNA motif” OR “DNA binding” OR “upstream region”)

2. SNPs and/or haplotypes: (Haplotype OR Polymorphism OR “single nucleotide polymorphism” OR “variable number of tandem repeat polymorphisms” OR “tandem repeats” OR “microsatellite polymorphisms” OR allele OR “genotypic variation” OR “genetic locus” OR “DNA polymorphism” OR “restriction fragment length polymorphism”)

3. Gene expression profiles/profiling: (“nucleic acid” OR nucleotide OR “nucleotide sequence” OR oligonucleotide OR deoxyribonucleotide OR “recombinant DNA” OR cDNA OR plasmid) AND (“gene expression profile” OR detection OR array OR screen OR “microarray” OR diagnostic OR treatment)

With U.S. class restriction: 800* OR 435* OR 424* OR 535* OR 935* OR 530* OR 514* OR 436*

4. Protein structure: (protein OR polypeptide OR oligopeptide or proteome OR protease OR enzymatic OR “enzymatic polypeptide” OR peptide OR “protein complex” OR “protein domain” OR PDB OR “protein data bank” OR motif OR antibody OR antibodies or enzyme) AND (“three-dimensional structure” OR angstrom OR “atomic coordinate” OR coordinate OR “space group” OR “binding pocket” OR “binding domain” OR “fold space” OR “modeling test compounds”) AND (“mass spectroscopy” OR MS OR “mass spectrometry” OR crystallography OR crystallographic OR NMR OR “nuclear magnetic resonance” OR “x-ray crystallography” OR “crystal structure” OR “computational modeling” OR “computer readable storage medium” OR algorithm OR “crystalline form” OR “in silico screening” )

5. Protein-protein interactions: (protein OR polypeptide OR oligopeptide OR peptide OR proteome OR protease OR enzymatic OR “enzymatic polypeptide” OR peptide OR “protein complex” OR “protein domain” OR PDB OR “protein data bank” OR motif OR antibody OR antibodies OR enzyme OR factor OR homolog OR homologue OR analog OR analogue OR ortholog OR orthologue) AND (“interaction partner” OR ((“protein-protein” OR “protein-DNA” OR “DNA-protein”) AND (binding or interaction or assembly)) OR “receptor-ligand” OR ((binding OR interaction OR interacting OR active) AND (domain OR site OR region OR pocket)) OR “receptor-agonist” OR “receptor/agonist” OR “re-

ceptor-antagonist” OR “receptor/antagonist” OR “receptor-target” OR “receptor/target” OR bivalent OR “agonist-antagonist” OR “agonist/antagonist”)

With U.S. class restriction: 800* OR 435* OR 424* OR 536* OR 935* OR 530* OR 514* OR 436*

6. Modified animals: ((Transgenic or “targeted deletion” or “targeted ablation” or knockout) NOT plant)

With U.S. class restriction: 800* OR 435* OR 424* OR 536* OR 935* OR 530* OR 514* OR 436*

7. Software: Software and protein OR software and genetics OR software and “nucleic acid” OR software and “systems biology” OR software and “protein regulation pathways” OR software and “protein regulation pathways” OR “evolutionary computation” and software OR “genetic programming” and software

With U.S. class restriction: 435

8. Algorithms: Algorithms and genetic OR algorithms and protein OR algorithms and haplotype OR algorithms and biological evolution OR “evolutionary computation” OR “genetic algorithms” OR “genetic programming” OR “modeling genetic inheritance” OR “biological evolution” and modeling OR “medical informatics” OR “sequencing algorithms” OR “informatics” and protein

With U.S. class restriction: 435

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