GlossaryΒΆ
- Study
- Represents a collection of samples and experiments applied to these samples.
- Sample
- A representation of the physical amount of material collected. It represents a specimen of a biome.
- Run
- The sequence file obtained from performing an experiment (an experiment generally includes several steps such as filtration, metatranscriptomic extraction and Illumina MiSeq sequencing, for example) on all or part of a sample. Several runs can therefore be generated from a single sample.
- Analysis result
- The end result of the pipeline analysis of a run.
- Biome
- An ecological community type. in EBI Metagenomics, biomes are organised hierarchically going from large types (such as soil, host-associated or aquatic) to more precise types (such as forest soil, skin or coastal) based on the GOLD classification
- Pipeline
- A prescribed set of successive steps needed to transform an input (raw reads for EBI Metagenomics) into an output with added information (annotated files with taxonomy and functional assignments for EBI Metagenomics) pipeline tool a software or script used during the individual step of an analysis pipeline.
- Go Term
- A defined vocabulary term to represent the functional attributes of a protein. Fine by the the Gene Ontology initiative, GO terms are organised hierarchically to unambiguously define the biological process, precise molecular function and cellular location of a protein.
- Go slim
- Go slim terms are cut-down version of the GO hierarchy to be able to give an overview of the functional results. It is used on EBI Metagenomics website. The GO slim hierarchy lacks the fine granularity of the full GO hierarchy.
- InterPro
- Combines protein signatures from a number of member databases into a single searchable resource, capitalising on their individual strengths to produce a powerful integrated database and diagnostic tool.
- Metagenomic
- Refer to environmental sample where Whole Genome Shotgun sequencing method have been applied. Analysis will yield taxonomic and functional information.
- Metatranscriptomic
- Refer to environmental sample where whole transcriptome sequencing method have been applied. Analysis will yield taxonomic and functional information.
- Amplicon
- Refer to environmental sample where a marker gene have been amplified and sequenced. On the EMG website, we use the term amplicon when the amplified marker gene is ribosomal RNA gene. Analysis will yield taxonomic information.
- Assembly
- Refer to environmental sample where Whole Genome Shotgun sequencing reads have been assembled to form larger fragments called contigs. Analysis will yield taxonomic and functional information.
- Metabarcoding
- Refer to environmental sample where a marker gene, different from ribosomal RNA gene, have been amplified and sequenced. Analysis will yield taxonomic information.
- Predicted coding sequences (pCDS)
- Partial or complete gene sequence as predicted by the gene caller (FragGenScan for read submissions, Prodigal and FragGenScan for assembly submissions)
- 16S rRNA genes
- Main prokaryotic ribosomal RNA genes used for taxonomic assignments.
- 18S rRNA genes
- Main eukaryotic ribosomal RNA genes used for taxonomic assignments.
- OTU
- Operational Taxonomic Unit representing a group of sequences sharing high similarity with each other.
- LSU, SSU
- Clusters of Large and Small Subunit ribosomal RNA genes. LSU comprises 23S (for prokaryotes) and 28S (for eukaryotes) sequences while the SSU represents 16S (for prokaryotes) and 18S (for eukaryotes) sequences.