source st
View samplesmost optional attributes removed
Template
Attributes
| Name | Type | Description | PID  | Unit |
|---|---|---|---|---|
| Source Name* | String | Sources are considered as the starting biological material used in a study. | - | - |
| Title* | String | Short text that can be used to call out sample records in search results or in displays. | - | - |
| Description* | String | Free-form text describing the sample, its origin, and its method of isolation. | - | - |
| tax_id* | String | NCBI Taxonomy Identifier number ID. This is appropriate for individual organisms and some environmental samples. | - | - |
| organism | String | Scientific name of sample that distinguishes its taxonomy. Please use a name or synonym that is tracked in the INSDC Taxonomy database. Also, this field can be used to confirm the TAXON_ID setting. | - | - |
| ploidy* | Controlled Vocabulary - ploidy (free text allowed) | The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). It has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2013-10-28) please refer to http://purl.bioontology.org/ontology/PATO. Mandatory for MIGS of eukaryotes. | - | - |
| number of replicons* | Integer | Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote. Mandatory for MIGS of eukaryotes, bacteria, archaea and segmented virus. | - | - |
| estimated size* | Integer | The estimated size of the genome (in bp) prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. Mandatory for MIGS of eukaryotes. | - | - |
| collection date* | String | The date of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid ISO8601 compliant times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008. | - | - |
| geographic location (country and/or sea)* | Controlled Vocabulary - geographic location (country and/or sea) (free text allowed) | The geographical origin of the sample as defined by the country or sea. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html). | - | - |
| geographic location (latitude)* | String | The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system | - | - |
| geographic location (longitude)* | String | The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system | - | - |
| isolation and growth condition* | String | Publication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material. Mandatory for MIGS and MIMARKS Specimen. | - | - |
| plant structure* | Controlled Vocabulary - plant structure (free text allowed) | name of plant structure that the sample was obtained from; for Plant Ontology (PO) terms see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051); if an individual flower is sampled the sex of it can be recorded here | - | - |
| plant developmental stage* | Controlled Vocabulary - plant developmental stage (free text allowed) | developmental stage at the time of sample collection; for Plant Ontology (PO) (v 20) terms, see http://purl.bioontology.org/ontology/PO, e.g. hypocotyl emergence stage (PO_0007043) | - | - |
| plant growth medium* | String | specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium, recommended value is a specific value from EO:plant growth medium or other controlled vocabulary | - | - |
| submission date | String | Date in which sample was submitted to ENA. | - | - |
| status | Controlled Vocabulary - status (free text allowed) | Status of submission to ENA. | - | - |
| accession | String | ENA sample accession code. Provided by ENA after submission. | - | - |
Tags
Not specifiedRelated items
Projects: Environmental stimuli on yeast, Mutant re-sequencing
Institutions: Default Institution
Projects: Environmental stimuli on yeast, Mutant re-sequencing
Web page: Not specified
Programme: Claire's research group
Public web page: Not specified
Characterizing the hi-per mutant line
Submitter: claire s
Studies: Study - Mutant re-sequencing
Assays: Assay - DNA extraction, Assay - Library preparation, Assay - Sequencing
In this Study we are re-sequencing a mutant line from our group to identify potential off target mutations.
Submitter: David s
Investigation: Investigation - hi-per characterization
Assays: Assay - DNA extraction, Assay - Library preparation, Assay - Sequencing
Source Name (String) *, Title (String) *, Description (String) *, tax_id (String) *, organism (String) , ploidy (Controlled Vocabulary - ploidy) *, number of replicons (Integer) *, extrachromosomal elements (Integer) , estimated size (Integer) *, collected_by (String) , collection date (String) *, geographic location (altitude) (String) , geographic location (country and/or sea) (Controlled Vocabulary - geographic location (country and/or sea)) *, geographic location (latitude) (String) *, geographic location (longitude) (String) *, geographic location (region and locality) (String) , identified_by (String) , geographic location (depth) (String) , environment (biome) (Controlled Vocabulary - environment (biome)) , environment (feature) (String) , geographic location (elevation) (String) , source material identifiers (String) , isolation and growth condition (String) *, propagation (String) , plant structure (Controlled Vocabulary - plant structure) *, plant developmental stage (Controlled Vocabulary - plant developmental stage) *, sampled age (String) , sample phenotype (String) , sample health state (Controlled Vocabulary - sample health state) , sample disease status (String) , sample disease stage (String) , sample wet mass (String) , sample dry mass (String) , sample height (String) , sample length (String) , growth facility (Controlled Vocabulary - growth facility) , sample capture status (Controlled Vocabulary - sample capture status) , genotype (String) , genetic modification (String) , organism common name (String) , subspecific genetic lineage rank (String) , subspecific genetic lineage name (String) , biological status (String) , organism phenotype (String) , ancestral data (String) , source material description (String) , biotic relationship (String) , growth habit (Controlled Vocabulary - growth habit) , plant sex (String) , climate environment (String) , gaseous environment (String) , seasonal environment (String) , soil_taxonomic/FAO classification (String) , soil_taxonomic/local classification (String) , soil_taxonomic/local classification method (String) , soil type (Controlled Vocabulary - soil type) , soil type method (String) , drainage classification (Controlled Vocabulary - drainage classification) , texture (String) , texture method (String) , soil water content (String) , soil pH (String) , plant growth medium (String) *, rooting conditions (String) , culture rooting medium (String) , rooting medium macronutrients (String) , rooting medium micronutrients (String) , rooting medium organic supplements (String) , rooting medium carbon (String) , rooting medium regulators (String) , rooting medium solidifier (String) , rooting medium pH (String) , air temperature regimen (String) , antibiotic regimen (String) , chemical mutagen (String) , fertilizer regimen (String) , fungicide regimen (String) , gravity (String) , growth hormone regimen (String) , herbicide regimen (String) , humidity regimen (String) , mineral nutrient regimen (String) , non-mineral nutrient regimen (String) , pesticide regimen (String) , pH regimen (String) , radiation regimen (String) , rainfall regimen (String) , salt regimen (String) , standing water regimen (String) , watering regimen (String) , water temperature regimen (String) , plant treatment (String) , light regimen (String) , biotic regimen (String) , mechanical damage (String) , chemical administration (String) , perturbation (String) , submission date (String) , status (Controlled Vocabulary - status) , accession (String)
