NOAA Omics working group keyword request

[elijah.hall]

Hello, Could you please add these additional 'omics terms to the GCMD?

Thank you,
Elijah Hall

Term: Microbiome
Hierarchy: Earth science > Biosphere > Omics
Definition: The microbiome is the community of microorganisms (such as fungi, bacteria, archaea, and viruses) that exists in a particular environment.
Documentation: https://www.genome.gov/genetics-glossary#M

Term: Holobiont
Hierarchy: Earth science > Biosphere > Omics > Microbiome
Definition: A host (e.g., a human) with all of its associated symbiotic organisms (e.g., a human’s microbiome).
Documentation: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6208839/#:~:text=This%20theory%20states%20that%20a,%2C%20a%20holobiont)%20in%20evolution.

Term: Proteomics
Hierarchy: Earth science > Biosphere > Omics
Definition: Proteomics is the study of the interactions, function, composition, and structures of proteins and their cellular activities. Proteomics provides a better understanding of the structure and function of an organism.
Documentation: https://www.tandfonline.com/doi/pdf/10.1080/02648725.1996.10647923

Term: Mitogenome (mitochondrial genome)
Hierarchy: Earth science > Biosphere > Omics
Definition: The entire DNA sequence, or genome, contained within the mitochondria that codes for part of the proteins constituting the organelle. Many genes present on the mitogenome are used as metabarcoding markers. Mitogenomes are double-stranded DNA molecules of variable size that generally are found as circular, linear, or branched forms. Each cell may contain more than 1,000 copies of a single mitogenome haplotype.
Documentation: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0273330; https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7194472/

Term: Epigenome/epigenetics
Hierarchy: Earth science > Biosphere > Omics
Definition: Epigenetics (also sometimes called epigenomics) is a field of study focused on changes in DNA that do not involve alterations to the underlying sequence. The DNA nucleotides and the proteins that interact with DNA can have chemical modifications that change the degree to which genes are turned on and off. Certain epigenetic modifications may be passed on from parent cell to daughter cell during cell division or from one generation to the next. The collection of all epigenetic changes in a genome is called an epigenome.
Documentation: https://www.genome.gov/genetics-glossary/Epigenetics

Term: Metabolomics
Hierarchy: Earth science > Biosphere > Omics
Definition: The comprehensive analysis of metabolites in a biological specimen which can provide detailed characterization of metabolic phenotypes.
Documentation: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4850886/

Term: Metadata
Hierarchy: Data format
Definition: Information describing the characteristics of data including, for example, structural metadata describing data structures (e.g., data format, syntax, and semantics) and descriptive metadata describing data contents (e.g., information security labels).
Documentation: https://csrc.nist.gov/glossary/term/metadata

Term: Genomic data
Hierarchy: Data format
Definition: Genomic data are data related to the structure and function of an organism's genome. The genome is all the cellular data an organism needs to grow and function. Genomic data include information like the sequence of molecules in an organism’s genes.
Documentation: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8501405/

Term: Raw genomic data
Hierarchy: Data format
Definition: Raw genomic data comprise genomic sequence data before annotation and interpretation. Raw genomic data includes sequences of DNA that are not yet aligned into complete genes or genomes. It typically is stored as FASTQ, BAM, or VCF files.
Documentation: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9328317/#:~:text=Raw%20genomic%20data%20comprise%20genomic,may%20reveal%20information%20of%20value

Term: FASTQ/FASTA
Hierarchy: Data format > Raw genomic data
Definition: Both FASTQ and FASTA are file formats designed to store sequence data. FASTA files only store sequence information, while FASTQ files store both sequence data and quality scores/values.
Documentation: https://compgenomr.github.io/book/fasta-and-fastq-formats.html

Term: Processed genomic data
Hierarchy: Data format
Definition: Processed data can encompass any number of data products, depending on the source. For metabarcoding, processed data can include a list of Amplicon sequence variants. For genomics, this could include the alignment of raw data to previously generated reference genomes, or potentially could involve a novel de novo assembly of a genome. For transcriptomics, this data could include expression estimates for genes in a genome. Note there are other applications of this terminology besides those listed here.
Documentation: https://gdc.cancer.gov/about-data/gdc-data-processing/genomic-data-processing

Term: Population Biology
Hierarchy: Earth science > Human dimensions > Population > Natality
Definition: The study of the ecology, evolution, and dynamics of populations, or groups of individuals within the same species.
Documentation: https://link.springer.com/book/10.1007/978-1-4757-2731-9

Term: Population genetics/genomics
Hierarchy: Earth science > Human dimensions > Population > Natality
Definition: An approach that surveys nucleotide variation across the genome within and between natural populations to identify loci that are divergent between populations and/or species.
Documentation: https://www.sciencedirect.com/science/article/pii/S0169534713001675

[GCMDx - sritz]

Hello Elijah, we will review your keyword request.

Scott Ritz
--
KBR | CMR Metadata Team Scrum Master
5700 Rivertech Ct| Riverdale, MD 20737 | USA
Scott.A.Ritz@nasa.gov

https://www.earthdata.nasa.gov/idn

[GCMDx - sritz]

Hello Elijah, all of the Science Keywords you requested will be published today 4/5/2024. The Science Team would like to spend a little more time discussing the Data Format keyword requests. I hope that is OK?

Scott Ritz

[GCMDx - sritz]

Actually, I did published one of the Data Format keywords. FASTQ/FASTA The others need some more discussion.

Scott

[GCMDx - sritz]

Hello @elijah.hall regarding these keywords that you requested to be Data Format keywords. We discussed these and they appear to describe types of data, but not actually Data Formats. A Format would be something like FASTQ, BAM, or VCF files... Can you share with is the formats that this data is held in?

Thanks

Scott

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Term: Metadata
Term: Genomic data
Term: Raw genomic data
Term: Processed genomic data