Systems and methods for annotating biomolecule data

Abstract

Systems, methods, software and computer-usable media for annotating biomolecule-related data are disclosed. In certain exemplified embodiments, the biomolecules can be nucleic acids and the data can be sequence-related data. In various embodiments, systems can include one or more public or private biological attributes (e.g., annotation information databases, data storage devices and systems, etc.) sources, one or more genomic features data sources (e.g., genomic variant tools, genomic variant databases, genomic variant data storage devices and systems, etc.), a computing device (e.g., workstation, server, personal computer, mobile device, etc.) hosting an annotations module and/or a reporting module, and a client terminal.

1 - 24 . (canceled) 
     
     
         25 . A system for annotating genomic features, comprising:
 a client terminal;   a first data source comprising data files or data records containing genomic features data associated with one or more genomic sequence positions within one or more regions of a genome;   a second data source comprising biological attributes data; and   a processor communicatively connected with the client terminal, the first data source and the second data source, the processor configured to:
 receive the genomic features data from the first data source, 
 search the second data source to identify one or more relevant biological attributes associated with the genomic features data received from the first data source, wherein the one or more biological attributes comprise a disease state, a therapeutic outcome, a metabolic pathway, a biological signaling pathway, a biological regulation pathway, or any combination thereof, 
 annotate the genomic features data associated with the one or more genomic sequence positions received from the first data source with the identified one or more biological attributes to create annotated genomic features data, wherein the annotated genomic features data include a new field added to the data file or the data record associated with the genomic feature, the new field containing annotations representing the identified biological attributes associated with the genomic features, 
 parse the annotated genomic features data to ascertain statistical trends, wherein the statistical trends include a first statistical trend related to a particular type of the genomic features within the genomic features data and a second statistical trend related to a particular type of the annotations representing the identified biological attributes associated with the genomic features in the annotated genomic features data, 
 configure the client terminal to display filter conditions selectable by a user, 
 receive a set of user-selected filter conditions from the client terminal, 
 query the annotations representing the identified biological attributes based on the set of user-selected filter conditions to select corresponding annotated genomic features data, and 
 display, at the client terminal, a report summarizing the corresponding annotated genomic features data and the ascertained statistical trends. 
   
     
     
         26 . The system, as recited in  claim 25 , wherein the processor is further configured to filter the annotated genomic features data based on one or more conditions to create filtered annotated genomic features data. 
     
     
         27 . The system, as recited in  claim 26 , wherein the one or more conditions relate to whether the annotated genomic feature overlaps an exon, whether the annotated genomic feature overlaps a gene, whether the annotated genomic feature is found in a designated data source, or any combination thereof. 
     
     
         28 . The system, as recited in  claim 27 , wherein the designated data source is a dbSNP database. 
     
     
         29 . The system, as recited in  claim 25 , wherein the processor is configured to identify relevant biological attributes based on whether the genomic feature is a marker for the biological attribute, an effect that the genomic feature has on the biological attribute, interrelationships between different genomic features, the biological attribute providing a characterization of the genomic feature, a correlation between the genomic feature and its position on a particular locus/chromosome, or any combination thereof. 
     
     
         30 . The system of  claim 25 , wherein the annotations are included in metadata associated with the data file or data record. 
     
     
         31 . The system of  claim 25 , wherein the processor is a component of at least one of a client device, a workstation, a server, a personal computer, and a mobile device. 
     
     
         32 . The system, as recited in  claim 29 , wherein the effect is an initiating response, a blocking response, a stimulatory response, an inhibitory response, or any combination thereof. 
     
     
         33 . The system, as recited in  claim 25 , wherein the genomic feature is a genetic mutation. 
     
     
         34 . The system, as recited in  claim 25 , further comprising a sequencing machine configured to generate nucleic acid sequencing data, wherein the sequencing machine is communicatively connected with a genomic variant identification tool configured to receive and convert the nucleic acid sequencing data into the genomic features data for the first data source. 
     
     
         35 . The system, as recited in  claim 34 , wherein the genomic features data comprises at least one genomic variant. 
     
     
         36 . A method for annotating genomic features, comprising:
 receiving, at a processor, genomic features data associated with one or more genomic sequence positions within one or more regions of a genome, the genomics features data received from a first data source comprising data files or data records containing the genomic features data;   searching one or more data sources to identify one or more relevant biological attributes associated with each of the genomic features based on a set of criteria, wherein the one or more biological attributes comprise a disease state, a therapeutic outcome, a metabolic pathway, a biological signaling pathway, a biological regulation pathway, or any combination thereof;   annotating, using the processor, the genomic features data associated with the one or more genomic sequence positions with the identified biological attributes to create annotated genomic features data, wherein the annotated genomic features data include a new field added to the data file or the data record associated with the genomic feature, the new field containing annotations representing the identified biological attributes associated with the genomic features;   parsing the annotated genomic features data to ascertain statistical trends, wherein the statistical trends include a first statistical trend related to a particular type of the genomic features within the genomic features data and a second statistical trend related to a particular type of the annotations representing the identified biological attributes associated with the genomic features in the annotated genomic features data;   configuring a client terminal to display filter conditions selectable by a user;   receiving a set of user-selected filter conditions from the client terminal;   querying the annotations representing the identified biological attributes based on the set of user-selected filter conditions to select corresponding annotated genomic features data; and   displaying, at the client terminal, a report summarizing the corresponding annotated genomic features data and the ascertained statistical trends.   
     
     
         37 . The method for annotating genomic features, as recited in  claim 36 , wherein identifying one or more relevant biological attributes is based on whether the genomic feature is a marker for the biological attribute, an effect that the genomic feature has on the biological attribute, interrelationships between different genomic features, the biological attribute providing a characterization of the genomic feature, a correlation between the genomic feature and its position on a particular locus/chromosome, or any combination thereof. 
     
     
         38 . The method for annotating genomic features, as recited in  claim 37 , wherein the effect is an initiating response, a blocking response, a stimulatory response, an inhibitory response, or any combination thereof. 
     
     
         39 . The method for annotating genomic features, as recited in  claim 36 , wherein the genomic feature is a genetic mutation. 
     
     
         40 . The method for annotating genomic features, as recited in  claim 36 , further comprising:
 filtering the annotated genomic features data based on one or more conditions to create filtered annotated genomic features data.   
     
     
         41 . The method for annotating genomic features, as recited in  claim 36 , wherein the annotations are included in metadata associated with the data file or data record. 
     
     
         42 . The method for annotating genomic features, as recited in  claim 36 , wherein the processor is a component of at least one of a client device, a workstation, a server, a personal computer, and a mobile device. 
     
     
         43 . The method for annotating genomic features, as recited in  claim 36 , further comprising:
 sequencing at least one nucleic acid to generate nucleic acid sequencing data; and   converting the nucleic acid sequencing data into the genomic features data.   
     
     
         44 . The method, as recited in  claim 40 , wherein the one or more conditions relate to whether the annotated genomic feature overlaps an exon, whether the annotated genomic feature overlaps a gene, whether the annotated genomic feature is found in a designated data source, or any combination thereof.