human-gut

v1.0.0 sample

SDRF template for human gut metaproteomics. Extends metaproteomics with host-associated columns aligned with the GSC MIxS human-gut extension (0016004). Combine with ms-proteomics for MS acquisition columns.

Key Guidance

The human-gut template adds host-associated metadata fields from the MIxS

human-gut extension. These columns describe the host organism, its health

status, diet, and other clinical context relevant to gut microbiome studies.

PRIDE ontology terms (PRIDE:0000674 children) include MIxS cross-references.

Usage: human-gut + ms-proteomics

Inheritance

base → metaproteomics → human-gut

Combination Rules

Mutually exclusive with: soil, water

Columns

21 own + 27 inherited = 48 total · click a row for details

	Column	Requirement	Source	Description
▶	source name	required	base	Unique identifier for the biological sample
Description Unique identifier for the biological sample Ontology PRIDE:0000623 Properties
▶	assay name	required	base	Unique identifier for the data acquisition run
Description Unique identifier for the data acquisition run Ontology NCIT:C178857 Properties
▶	technology type	required	base	Type of technology used
Description Type of technology used Ontology PRIDE:0000663 Properties Validators single_cardinality_validator values — values: `proteomic profiling by mass spectrometry`, `protein expression profiling by antibody array`, `protein expression profiling by aptamer array`
▶	comment[technical replicate]	required	base	Identifier for the technical replicate (integer starting from 1)
Description Identifier for the technical replicate (integer starting from 1) Ontology MS:1001808 Properties type: integer
▶	comment[data file]	required	base	Name of the raw data file
Description Name of the raw data file Ontology MS:1003083 Properties
▶	characteristics[environmental sample type]	required	metaproteomics	Type of environmental sample analyzed (ENVO or EFO term). Corresponds to MIxS env_medium (MIXS:0000014).
Description Type of environmental sample analyzed (ENVO or EFO term). Corresponds to MIxS env_medium (MIXS:0000014). Ontology PRIDE:0000993 Properties Validators ontology — ontologies: envo, efo Should be a valid ENVO or EFO term Examples `soil`, `seawater`, `gut microbiome`, `wastewater`, `biofilm`
▶	characteristics[host organism]	required	human-gut	Host organism for host-associated microbiome samples
Description Host organism for host-associated microbiome samples Ontology PRIDE:0000998 Properties allows N/A Validators ontology — ontologies: ncbitaxon Should be a valid NCBI Taxonomy term Examples `Homo sapiens`
▶	comment[sdrf version]	recommended	base	Version of the SDRF-Proteomics specification used to annotate this file
Description Version of the SDRF-Proteomics specification used to annotate this file Ontology PRIDE:0000839 Properties Validators semver SDRF specification version Examples `v1.1.0`, `v2.0.0-dev`
▶	characteristics[geographic location]	recommended	metaproteomics	Geographic location where sample was collected (GAZ term or coordinates). Corresponds to MIxS geo...
Description Geographic location where sample was collected (GAZ term or coordinates). Corresponds to MIxS geo_loc_name (MIXS:0000010). Ontology PRIDE:0000995 Properties allows N/A allows not available Validators ontology — ontologies: gaz Should be a valid GAZ term or coordinates Examples `Pacific Ocean`, `Amazon rainforest`, `47.6062 N, 122.3321 W`
▶	characteristics[environmental medium]	recommended	metaproteomics	Environmental material from which the sample was obtained (ENVO term). Corresponds to MIxS env_me...
Description Environmental material from which the sample was obtained (ENVO term). Corresponds to MIxS env_medium (MIXS:0000014). Ontology PRIDE:0000994 Properties allows N/A allows not available Validators ontology — ontologies: envo Should be a valid ENVO environmental material term Examples `soil`, `seawater`, `freshwater`, `feces`, `biofilm`
▶	characteristics[host subject id]	recommended	human-gut	De-identified unique identifier for the host subject. Corresponds to MIxS host_subject_id (MIXS:0000861).
Description De-identified unique identifier for the host subject. Corresponds to MIxS host_subject_id (MIXS:0000861). Ontology PRIDE:0000680 Properties allows N/A allows not available Validators identifier Host subject identifier Examples `subject_001`, `patient_A`, `anonymized`
▶	characteristics[host disease status]	recommended	human-gut	Host disease diagnoses. Corresponds to MIxS host_disease_stat (MIXS:0000031).
Description Host disease diagnoses. Corresponds to MIxS host_disease_stat (MIXS:0000031). Ontology PRIDE:0000682 Properties allows N/A allows not available Validators ontology — ontologies: mondo, doid Should be a valid disease ontology term Examples `inflammatory bowel disease`, `colorectal cancer`, `healthy`
▶	characteristics[host body site]	recommended	human-gut	Body site where sample was obtained. Corresponds to MIxS host_body_site (MIXS:0000867).
Description Body site where sample was obtained. Corresponds to MIxS host_body_site (MIXS:0000867). Ontology PRIDE:0000685 Properties allows N/A allows not available Validators ontology — ontologies: uberon, bto Body site should be a valid UBERON or BTO term Examples `stool`, `oral cavity`, `colon`
▶	comment[sdrf template]	optional	base	Template name and version used for annotation. Two formats are supported - key=value format (NT=t...
Description Template name and version used for annotation. Two formats are supported - key=value format (NT=template_name;VV=vX.Y.Z) or simple format (template_name vX.Y.Z). Multiple templates can be specified using multiple columns. Ontology PRIDE:0000832 Properties allows not available multiple cardinality Validators pattern — pattern: `^(NT=[\w-]+;VV=v\d+\.\d+\.\d+(-[\w.]+)?\|[\w-]+ v\d+\.\d+\.\d+(-[\w.]+)?)$` Template can be specified as 'NT=name;VV=vX.Y.Z' or 'name vX.Y.Z' Examples `NT=human;VV=v1.1.0`, `human v1.1.0`, `NT=ms-proteomics;VV=v1.1.0`, `ms-proteomics v1.1.0`
▶	comment[sdrf annotation tool]	optional	base	Software tool or method used to generate or annotate the SDRF file. Two formats are supported - k...
Description Software tool or method used to generate or annotate the SDRF file. Two formats are supported - key=value format (NT=tool_name;VV=vX.Y.Z) or simple format (tool_name vX.Y.Z). Ontology PRIDE:0000840 Properties allows not available Validators pattern — pattern: `^(NT=[\w-]+;VV=v[\d.]+[\w.-]\|[\w-]+ v[\d.]+[\w.-]\|manual curation)$` Annotation tool can be specified as 'NT=name;VV=vX.Y.Z' or 'name vX.Y.Z' or 'manual curation' Examples `NT=lesSDRF;VV=v0.1.0`, `lesSDRF v0.1.0`, `NT=sdrf-pipelines;VV=v1.0.0`, `sdrf-pipelines v1.0.0`, `manual curation`
▶	comment[sdrf validation hash]	optional	base	Hash value for SDRF validation integrity checking
Description Hash value for SDRF validation integrity checking Properties allows N/A allows not available Validators pattern — pattern: `^.+$` Validation hash string
▶	characteristics[collection date]	optional	metaproteomics	Date when sample was collected (ISO 8601)
Description Date when sample was collected (ISO 8601) Ontology PRIDE:0000996 Properties allows N/A allows not available Validators date Sample collection date Examples `2024`, `2024-01`, `2024-01-15`
▶	characteristics[sample collection method]	optional	metaproteomics	Method used to collect the environmental sample
Description Method used to collect the environmental sample Ontology PRIDE:0000997 Properties allows N/A allows not available Validators pattern — pattern: `^.+$` Collection method description Examples `grab sample`, `core sample`, `swab`, `filtration`
▶	characteristics[depth]	optional	metaproteomics	Depth at which sample was collected. Corresponds to MIxS depth (MIXS:0000018).
Description Depth at which sample was collected. Corresponds to MIxS depth (MIXS:0000018). Ontology PRIDE:0000711 Properties allows N/A allows not available Validators number_with_unit Depth with unit Examples `10 m`, `50 cm`, `100 m`
▶	characteristics[altitude]	optional	metaproteomics	Altitude or elevation of sampling site. Corresponds to MIxS elevation (MIXS:0000093).
Description Altitude or elevation of sampling site. Corresponds to MIxS elevation (MIXS:0000093). Ontology PRIDE:0000712 Properties allows N/A allows not available Validators number_with_unit Altitude with unit Examples `500 m`, `1200 m`, `0 m`
▶	characteristics[temperature]	optional	metaproteomics	Temperature at sampling location. Corresponds to MIxS temperature (MIXS:0000113).
Description Temperature at sampling location. Corresponds to MIxS temperature (MIXS:0000113). Ontology PRIDE:0000703 Properties allows N/A allows not available Validators number_with_unit Temperature in Celsius Examples `25 °C`, `4 °C`, `-20 °C`
▶	characteristics[ph]	optional	metaproteomics	pH at sampling location
Description pH at sampling location Ontology PRIDE:0000746 Properties allows N/A allows not available Validators pattern — pattern: `^\d+(\.\d+)?$` pH value Examples `7.0`, `5.5`, `8.2`
▶	characteristics[sample storage]	optional	metaproteomics	Storage conditions for the sample before analysis
Description Storage conditions for the sample before analysis Ontology PRIDE:0000730 Properties allows N/A allows not available Validators pattern — pattern: `^.+$` Storage conditions Examples `-80C`, `liquid nitrogen`, `4C`
▶	comment[metagenome accession]	optional	metaproteomics	Accession number for matched metagenome data
Description Accession number for matched metagenome data Ontology PRIDE:0000956 Properties allows N/A allows not available Validators accession Database accession number Examples `MGYA00001234`, `SRP123456`
▶	characteristics[microbiome source]	optional	metaproteomics	Source of the microbiome being studied (e.g., gut microbiome, rhizosphere microbiome)
Description Source of the microbiome being studied (e.g., gut microbiome, rhizosphere microbiome) Ontology PRIDE:0000986 Properties allows N/A allows not available Validators pattern — pattern: `^.+$` Microbiome source description Examples `gut microbiome`, `rhizosphere microbiome`, `oral microbiome`, `skin microbiome`
▶	characteristics[biomass estimation]	optional	metaproteomics	Estimated microbial biomass in the sample
Description Estimated microbial biomass in the sample Ontology PRIDE:0000990 Properties allows N/A allows not available Validators pattern — pattern: `^.+$` Biomass estimation Examples `1e9 cells/g`, `high biomass`, `low biomass`
▶	characteristics[host contamination]	optional	metaproteomics	Level of host protein contamination if known
Description Level of host protein contamination if known Ontology PRIDE:0000991 Properties allows N/A allows not available Validators pattern — pattern: `^.+$` Host contamination level Examples `low (<5%)`, `moderate (5-20%)`, `high (>20%)`
▶	comment[contaminant database]	optional	metaproteomics	Contaminant database(s) used in database search
Description Contaminant database(s) used in database search Ontology PRIDE:0000992 Properties allows N/A allows not available Validators pattern — pattern: `^.+$` Contaminant database name(s) Examples `cRAP`, `MaxQuant contaminants`, `cRAP;MaxQuant contaminants`
▶	characteristics[mock community]	optional	metaproteomics	Identifier or name of mock community standard used
Description Identifier or name of mock community standard used Ontology PRIDE:0000987 Properties allows N/A allows not available Validators pattern — pattern: `^.+$` Mock community identifier Examples `ZymoBIOMICS Microbial Community Standard`, `ATCC MSA-1000`
▶	characteristics[mock community composition]	optional	metaproteomics	Description of mock community composition (species and ratios)
Description Description of mock community composition (species and ratios) Ontology PRIDE:0000988 Properties allows N/A allows not available Validators pattern — pattern: `^.+$` Community composition description Examples `8 bacteria + 2 yeasts at defined ratios`, `even mix of 10 species`
▶	comment[expected organism list]	optional	metaproteomics	Semicolon-separated list of organisms expected in mock community
Description Semicolon-separated list of organisms expected in mock community Ontology PRIDE:0000989 Properties allows N/A allows not available Validators pattern — pattern: `^.+$` Semicolon-separated organism list Examples `E. coli;B. subtilis;S. cerevisiae;L. fermentum`, `Bacillus subtilis;Staphylococcus aureus`
▶	characteristics[host age]	optional	human-gut	Age of host at the time of sampling. Corresponds to MIxS host_age (MIXS:0000255).
Description Age of host at the time of sampling. Corresponds to MIxS host_age (MIXS:0000255). Ontology PRIDE:0000681 Properties allows N/A allows not available Validators pattern — pattern: `^\d+[YMWDH]$` Age in standard format (Y=year, M=month, W=week, D=day, H=hour) Examples `45Y`, `8W`, `3M`
▶	characteristics[host sex]	optional	human-gut	Sex of the host organism. Corresponds to MIxS host_sex (MIXS:0000811).
Description Sex of the host organism. Corresponds to MIxS host_sex (MIXS:0000811). Ontology PRIDE:0000999 Properties allows N/A allows not available Validators values — values: `male`, `female`, `intersex` Host sex
▶	characteristics[host body-mass index]	optional	human-gut	Body mass index (weight/height^2). Corresponds to MIxS host_body_mass_index (MIXS:0000317).
Description Body mass index (weight/height^2). Corresponds to MIxS host_body_mass_index (MIXS:0000317). Ontology PRIDE:0000695 Properties allows N/A allows not available Validators pattern — pattern: `^[\d.]+$` BMI numeric value Examples `22.5`, `30.1`, `18.5`
▶	characteristics[host height]	optional	human-gut	Height of the host. Corresponds to MIxS host_height (MIXS:0000264).
Description Height of the host. Corresponds to MIxS host_height (MIXS:0000264). Ontology PRIDE:0000688 Properties allows N/A allows not available Validators number_with_unit Host height with unit Examples `175 cm`, `1.75 m`
▶	characteristics[host total mass]	optional	human-gut	Total mass of the host. Corresponds to MIxS host_tot_mass (MIXS:0000263).
Description Total mass of the host. Corresponds to MIxS host_tot_mass (MIXS:0000263). Ontology PRIDE:0000687 Properties allows N/A allows not available Validators number_with_unit Host mass with unit Examples `70 kg`, `85 kg`
▶	characteristics[ethnicity]	optional	human-gut	Ethnicity of the host. Corresponds to MIxS ethnicity (MIXS:0000895).
Description Ethnicity of the host. Corresponds to MIxS ethnicity (MIXS:0000895). Ontology PRIDE:0000696 Properties allows N/A allows not available Validators pattern — pattern: `^.+$` Ethnicity description Examples `European`, `East Asian`, `African`
▶	characteristics[host diet]	optional	human-gut	Diet type of the host. Corresponds to MIxS host_diet (MIXS:0000869).
Description Diet type of the host. Corresponds to MIxS host_diet (MIXS:0000869). Ontology PRIDE:0000689 Properties allows N/A allows not available Validators pattern — pattern: `^.+$` Diet description Examples `omnivore`, `vegan`, `western diet`, `high-fiber`
▶	characteristics[special diet]	optional	human-gut	Special dietary restrictions. Corresponds to MIxS special_diet (MIXS:0000905).
Description Special dietary restrictions. Corresponds to MIxS special_diet (MIXS:0000905). Ontology PRIDE:0000679 Properties allows N/A allows not available Validators pattern — pattern: `^.+$` Special diet description Examples `gluten-free`, `low FODMAP`, `ketogenic`
▶	characteristics[host last meal]	optional	human-gut	Content of last meal and time since feeding. Corresponds to MIxS host_last_meal (MIXS:0000870).
Description Content of last meal and time since feeding. Corresponds to MIxS host_last_meal (MIXS:0000870). Ontology PRIDE:0000690 Properties allows N/A allows not available Validators pattern — pattern: `^.+$` Last meal description Examples `breakfast 4 hours prior`, `fasting 12 hours`
▶	characteristics[gastrointestinal tract disorder]	optional	human-gut	History of GI tract disorders. Corresponds to MIxS gastroint_disord (MIXS:0000280).
Description History of GI tract disorders. Corresponds to MIxS gastroint_disord (MIXS:0000280). Ontology PRIDE:0000677 Properties allows N/A allows not available Validators pattern — pattern: `^.+$` GI disorder description Examples `Crohn's disease`, `ulcerative colitis`, `irritable bowel syndrome`, `none`
▶	characteristics[liver disorder]	optional	human-gut	History of liver disorders. Corresponds to MIxS liver_disord (MIXS:0000282).
Description History of liver disorders. Corresponds to MIxS liver_disord (MIXS:0000282). Ontology PRIDE:0000678 Properties allows N/A allows not available Validators pattern — pattern: `^.+$` Liver disorder description Examples `none`, `fatty liver disease`, `hepatitis`
▶	characteristics[antibiotic treatment]	optional	human-gut	Recent antibiotic exposure of the host
Description Recent antibiotic exposure of the host Ontology PRIDE:0001000 Properties allows N/A allows not available Validators pattern — pattern: `^.+$` Antibiotic treatment description Examples `none`, `amoxicillin 7 days prior`, `broad-spectrum`
▶	characteristics[ihmc medication code]	optional	human-gut	Medication codes (IHMC). Corresponds to MIxS ihmc_medication_code (MIXS:0000884).
Description Medication codes (IHMC). Corresponds to MIxS ihmc_medication_code (MIXS:0000884). Ontology PRIDE:0000683 Properties allows N/A allows not available Validators pattern — pattern: `^.+$` Medication code(s) Examples `none`, `A02BC01`, `N02BE01`
▶	characteristics[host body product]	optional	human-gut	Substance produced by the body where sample was obtained. Corresponds to MIxS host_body_product (...
Description Substance produced by the body where sample was obtained. Corresponds to MIxS host_body_product (MIXS:0000888). Ontology PRIDE:0000686 Properties allows N/A allows not available Validators pattern — pattern: `^.+$` Body product description Examples `stool`, `mucus`, `saliva`
▶	characteristics[host body temperature]	optional	human-gut	Core body temperature at sample collection. Corresponds to MIxS host_body_temp (MIXS:0000874).
Description Core body temperature at sample collection. Corresponds to MIxS host_body_temp (MIXS:0000874). Ontology PRIDE:0000694 Properties allows N/A allows not available Validators number_with_unit Body temperature in Celsius Examples `36.6 °C`, `37.2 °C`
▶	characteristics[perturbation]	optional	human-gut	Type of perturbation applied. Corresponds to MIxS perturbation (MIXS:0000754).
Description Type of perturbation applied. Corresponds to MIxS perturbation (MIXS:0000754). Ontology PRIDE:0000700 Properties allows N/A allows not available Validators pattern — pattern: `^.+$` Perturbation description Examples `antibiotic administration`, `dietary intervention`, `none`
▶	characteristics[chemical administration]	optional	human-gut	Chemical compounds administered to the host. Corresponds to MIxS chem_administration (MIXS:0000751).
Description Chemical compounds administered to the host. Corresponds to MIxS chem_administration (MIXS:0000751). Ontology PRIDE:0000684 Properties allows N/A allows not available Validators pattern — pattern: `^.+$` Chemical administration description Examples `metformin 500mg daily`, `probiotics`, `none`

Contributors

Yasset Perez-Riverol (yperez@ebi.ac.uk) - EMBL-EBI
Deepti Jaiswal Kundu (jaiswal@ebi.ac.uk) - EMBL-EBI
Nithu Sara John (nithu@ebi.ac.uk) - EMBL-EBI
Nandana Madhusoodanan (nandana@ebi.ac.uk) - EMBL-EBI
Asier Larrea (alarre@ebi.ac.uk) - EMBL-EBI
Toan Phung (TPhung001@dundee.ac.uk) - University of Dundee
Timo Sachsenberg (timo.sachsenberg@uni-tuebingen.de) - University of Tübingen