Building a community-driven bioinformatics platform to facilitate Cannabis sativa multi-omics research.
Global changes in cannabis legislation after decades of stringent regulation and heightened demand for its industrial and medicinal applications have spurred recent genetic and genomics research. An international research community emerged and identified the need for a web portal to host cannabis-specific datasets that seamlessly integrates multiple data sources and serves omics-type analyses, fostering information sharing. The Tripal platform was used to host public genome assemblies, gene annotations, quantitative trait loci and genetic maps, gene and protein expression data, metabolic profiles and their sample attributes. Single nucleotide polymorphisms were called using public resequencing datasets on three genomes. Additional applications, such as SNP-Seek and MapManJS, were embedded into Tripal. A multi-omics data integration web-service Application Programming Interface (API), developed on top of existing Tripal modules, returns generic tables of samples, properties and values. Use cases demonstrate the API's utility for various omics analyses, enabling researchers to perform multi-omics analyses efficiently.
Pubmed ID: 39469541 RIS Download
Research resources used in this publication
- Crop Ontology (RRID:SCR_010299) (data or information resource)
- Pandas (RRID:SCR_018214) (software resource)
- Weighted Gene Co-expression Network Analysis (RRID:SCR_003302) (software resource)
- Jupyter Notebook (RRID:SCR_018315) (web application)
- ComBat (RRID:SCR_010974) (software resource)
- PLINK (RRID:SCR_001757) (software resource)
- BLASTN (RRID:SCR_001598) (data analysis service)
- MapMan (RRID:SCR_003543) (software resource)
- SAMtools/BCFtools (RRID:SCR_005227) (software resource)
- Salmon (RRID:SCR_017036) (software resource)
- GMAP (RRID:SCR_008992) (software resource)
- InterProScan (RRID:SCR_005829) (software resource)
- rnaSPAdes (RRID:SCR_016992) (software resource)
- TransDecoder (RRID:SCR_017647) (data processing software)
- MMseqs2 (RRID:SCR_022962) (software resource)
- GATK (RRID:SCR_001876) (software resource)
- gffread (RRID:SCR_018965) (data processing software)
- InterPro (RRID:SCR_006695) (software resource)
- CannSeek Database of Cannabis sativa SNPs (RRID:SCR_025579) (database)
- Trimmomatic (RRID:SCR_011848) (data processing software)
- Gene Expression Omnibus (GEO) (RRID:SCR_005012) (data repository)
- OBO (RRID:SCR_007083) (data or information resource)
- UniProt (RRID:SCR_002380) (data or information resource)
- RefSeq (RRID:SCR_003496) (data or information resource)
- NCBI BLAST (RRID:SCR_004870) (software resource)
- InterMine (RRID:SCR_001772) (software resource)
- Chado (RRID:SCR_024073) (software resource)
- JBrowse (RRID:SCR_001004) (software resource)
- MetaCyc (RRID:SCR_007778) (data or information resource)
- NCBI Sequence Read Archive (SRA) (RRID:SCR_004891) (data repository)
Additional research tools detected in this publication
Antibodies used in this publication
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This is a list of tools and resources that we have found mentioned in this publication.
Gene Ontology (tool)
RRID:SCR_002811
Computable knowledge regarding functions of genes and gene products. GO resources include biomedical ontologies that cover molecular domains of all life forms as well as extensive compilations of gene product annotations to these ontologies that provide largely species-neutral, comprehensive statements about what gene products do. Used to standardize representation of gene and gene product attributes across species and databases.
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RRID:SCR_022067
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RRID:SCR_010299
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RRID:SCR_018214
Software Python package for data analysis providing labeled data structures similar to R data. Provides data structures designed to make working with relational or labeled data. Software as building block for doing practical, real world open source data analysis and manipulation tool.
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RRID:SCR_003302
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RRID:SCR_018315
Open source web application to create and share documents that contain live code, equations, visualizations and narrative text. Used for data cleaning and transformation, numerical simulation, statistical modeling, data visualization, machine learning.
View all literature mentionsComBat (software resource)
RRID:SCR_010974
Adjusting batch effects in microarray expression data using Empirical Bayes methods.
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RRID:SCR_001757
Open source whole genome association analysis toolset, designed to perform range of basic, large scale analyses in computationally efficient manner. Used for analysis of genotype/phenotype data. Through integration with gPLINK and Haploview, there is some support for subsequent visualization, annotation and storage of results. PLINK 1.9 is improved and second generation of the software.
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RRID:SCR_001598
Web application to search nucleotide databases using a nucleotide query. Algorithms: blastn, megablast, discontiguous megablast.
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RRID:SCR_003543
Software tool that displays large genomics datasets (e.g. gene expression data from Arabidopsis Affymetrix arrays) onto diagrams of metabolic pathways or other biological processes.
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RRID:SCR_005227
Provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
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RRID:SCR_017036
Software tool for quantifying expression of transcripts using RNA-seq data. Provides fast and bias-aware quantification of transcript expression. Transcriptome-wide quantifier to correct for fragment GC-content bias.
View all literature mentionsGMAP (software resource)
RRID:SCR_008992
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. A software program for mapping and aligning cDNA sequences to a genome. The program maps and aligns a single sequence with minimal startup time and memory requirements, and provides fast batch processing of large sequence sets. The program generates accurate gene structures, even in the presence of substantial polymorphisms and sequence errors, without using probabilistic splice site models. Methodology underlying the program includes a minimal sampling strategy for genomic mapping, oligomer chaining for approximate alignment, sandwich DP for splice site detection, and microexon identification with statistical significance testing.
View all literature mentionsInterProScan (software resource)
RRID:SCR_005829
Software package for functional analysis of sequences by classifying them into families and predicting presence of domains and sites. Scans sequences against InterPro's signatures. Characterizes nucleotide or protein function by matching it with models from several different databases. Used in large scale analysis of whole proteomes, genomes and metagenomes. Available as Web based version and standalone Perl version and SOAP Web Service.
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RRID:SCR_016992
Software tool for assembling transcripts from RNA-Seq data. Explores surprising computational parallels between assembly of transcriptomes and single cell genomes. Suitable for all kind of organisms. Part of SPAdes package since version 3.9.
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RRID:SCR_017647
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RRID:SCR_022962
Software suite for ultra fast and sensitive sequence search and clustering. Used to search and cluster huge protein and nucleotide sequence sets. Designed to run on multiple cores and servers.
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RRID:SCR_001876
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View all literature mentionsgffread (data processing software)
RRID:SCR_018965
Open source software tool to manipulate files in GFF format. Used to convert, sort, filter, transform, or cluster genomic features.
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RRID:SCR_006695
Service providing functional analysis of proteins by classifying them into families and predicting domains and important sites. They combine protein signatures from a number of member databases into a single searchable resource, capitalizing on their individual strengths to produce a powerful integrated database and diagnostic tool. This integrated database of predictive protein signatures is used for the classification and automatic annotation of proteins and genomes. InterPro classifies sequences at superfamily, family and subfamily levels, predicting the occurrence of functional domains, repeats and important sites. InterPro adds in-depth annotation, including GO terms, to the protein signatures. You can access the data programmatically, via Web Services. The member databases use a number of approaches: # ProDom: provider of sequence-clusters built from UniProtKB using PSI-BLAST. # PROSITE patterns: provider of simple regular expressions. # PROSITE and HAMAP profiles: provide sequence matrices. # PRINTS provider of fingerprints, which are groups of aligned, un-weighted Position Specific Sequence Matrices (PSSMs). # PANTHER, PIRSF, Pfam, SMART, TIGRFAMs, Gene3D and SUPERFAMILY: are providers of hidden Markov models (HMMs). Your contributions are welcome. You are encouraged to use the ''''Add your annotation'''' button on InterPro entry pages to suggest updated or improved annotation for individual InterPro entries.
View all literature mentionsCannSeek Database of Cannabis sativa SNPs (database)
RRID:SCR_025579
Database of Cannabis sativa Single Nucleotide Polymorphisms discovered from NGS sequences and BioSamples available in NCBI. Sequence reads were called against cs10, Purple kush, and Finola reference assemblies using GATK and Parabricks pipelines.
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RRID:SCR_011848
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RRID:SCR_005012
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RRID:SCR_007083
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RRID:SCR_002380
Collection of data of protein sequence and functional information. Resource for protein sequence and annotation data. Consortium for preservation of the UniProt databases: UniProt Knowledgebase (UniProtKB), UniProt Reference Clusters (UniRef), and UniProt Archive (UniParc), UniProt Proteomes. Collaboration between European Bioinformatics Institute (EMBL-EBI), SIB Swiss Institute of Bioinformatics and Protein Information Resource. Swiss-Prot is a curated subset of UniProtKB.
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RRID:SCR_003496
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RRID:SCR_004870
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RRID:SCR_001772
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RRID:SCR_024073
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RRID:SCR_001004
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View all literature mentionsMetaCyc (data or information resource)
RRID:SCR_007778
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View all literature mentionsNCBI Sequence Read Archive (SRA) (data repository)
RRID:SCR_004891
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