Wikidata:WikiProject Microbiology/Properties
Properties accepted
Gram staining
In the prokaryotic lineages you can have gram +/- depending on the cell wall type. A property is currently not available for gram staining but the item pages are present to which can be linked to. For gram-positive the page is Q857288 and for gram-negative the page is Q632006
Property | Label | Data type | Expected value |
---|---|---|---|
Property:P2597 | Gram staining | item | Gram positive Q857288
Gram negative Q632006 |
Naming of organisms
There is a lengthy discussion going on in the PhenoBot "approval" page on how to name microbes and I think that this particular discussion should be continued either there or on another general area.
General organism properties
Here is a list of general used properties that could be used for microbes and other organisms.
Property | Label | Data type | Expected value |
---|---|---|---|
Property:P105 | taxon rank | item | Family, Genus, Species items see full list below |
Property:P685 | NCBI Taxonomy ID | item | Should theoretically always be there |
Unknown | UniProt Taxonomy ID | String | External reference |
Unknown | NCBI Bioproject ID | String | External reference |
Property:P225 | taxon name | String | Name matching the given taxon identifier |
Property:P171 | parent taxon | item | Should theoretically always be there |
Property:P31 | instance of | item | Q16521 |
Unknown | type strain | boolean | which item? Q3707858? |
Property:P2043 | length | integer | 902320 bp Q21481789 |
Unknown | GC content | float | with method specified as string? |
Biosafety
Is possible with the current biosafety properties
There are 4 levels of biosafety that shows the severity of precautions that are required to work with biological agents. Biosafety level 1 is the weakest form of containment and is often allocated for well characterised non-harmful organisms whereas biosafety level 4 is for the most pathogenic organisms such as the Ebola virus.
The property used for biosafety is the already defined P1604 with the corresponding levels 1, Q18396533, 2, Q18396535, 3, Q18396538 and 4 Q18396539
Property | Label | Data type | Expected value |
---|---|---|---|
Property: P1604 | biosafety level | item | Level 1 Q18396533
Level 2 Q18396535 Level 3 Q18396538 Level 4 Q18396539 |
Pathogenicity
Is not yet possible with the WD properties
This is intwined with biosafety in a biological sense. If an organism is pathogenic it is most likely not biosafety level 1 but it might not yet known to what other level it belongs to. However it is most likely known wether it is pathogenic to plants, animals and / or to humans.
Property | Label | Data type | Expected value |
---|---|---|---|
Unknown | Pathogenic to | item | Pointing to the corresponding organisms most likely via the taxon identifiers |
Growth Conditions
Motility
Is not yet possible with the WD properties
The ability of an organism to move spontaneously and actively can be described using various statements
Property | Label | Data type | Expected value |
---|---|---|---|
Unknown | Motility | item | Chemotactic (Chemotaxis) Q658145
Motile Q3359 Nonmotile (not yet found) |
Environment
Is not yet possible with the WD properties
This section might need further expansion and separation as the environment is a very broad range of what is possible. For smaller organisms this can be for example soil, ocean but also human or gut of certain animals. The environment can be further specified when this information is present. To give an example, these are the environments identified for a certain number of species and it is only a snapshot of the dataset that could be integrated into WD.
2804 | soil with plant residues |
2617 | soil |
188 | spacecraft-associated clean room class ISO 8, Herschel Space Observatory |
152 | unknown |
140 | seawater |
138 | marine sediment |
118 | soil with lime pebbles and plant residues |
114 | forest soil |
113 | soil with plant residues and lime pebbles |
For example one of the conditions for smaller organisms can be salinity which basically indicates the amount of salt in water.
Temperature range
Is not yet possible with the WD properties
The range of temperature an organism can survive in is currently described into four different groups (hyperthermophilic, mesophilic, psychrophilic, thermophilic) A property is currently not defined to store the range an organism can thrive in.
The current item pages are however still lacking integer information regarding the temperature ranges which can be added if such property is defined
Property | Label | Data type | Expected value |
---|---|---|---|
Unknown | Temperature optimum | integer | Optimal temperature for organism under normal conditions |
Unknown | Temperature minimum | integer | Minimum temperature for organism under normal conditions |
Unknown | Temperature maximum | integer | Maximum temperature for organism under normal conditions |
Unknown | Temperature range | item | Hyperthermophile Q1784119
Mesophile Q669652 Psychrophile Q913343 Thermophile Q834023 |
Oxygen requirement
Is not yet possible with the WD properties
Not all organisms can survive with or without oxygen and these definitions are currently defined by certain resources:
Property | Label | Data type | Expected value |
---|---|---|---|
Unknown | Oxygen requirement | item | Anaerobic Q189790
Aerobic Q193124 Microaerophilic Q548321 Facultative Q5428855 Facultative anaerobe Q1091848 Microaerophilic Q548321 Obligate aerobe Q7075150 Obligate anaerobe Q2915932 |
Oxygen requirement
Description | Requirement of oxygen for micro-organisms |
---|---|
Data type | Item |
Domain | taxon (Q16521) AND strain (Q855769) |
Allowed values | anaerobic organism (Q189790) OR aerobic organism (Q193124) OR microaerophile (Q548321) OR Facultative (Q5428855) OR facultative anaerobic organism (Q1091848) OR microaerophile (Q548321) OR obligate aerobe (Q7075150) OR obligate anaerobe (Q2915932) |
Example | Pseudomonas putida KT2440 (Q21079489) → aerobic organism (Q193124) |
Robot and gadget jobs | We are planning this to use in bots that add phenotypic characterisations |
- Motivation
Micro-organisms can grow under various oxygen conditions. Some can grow only with oxygen while others can only grow without. Between these two there is a range in which organisms can grow partially with or without oxygen. These phenotypic characterisations are of utmost interest for further characterising bacteria. jjkoehorst (talk) 06:54, 9 March 2016 (UTC)
- Hi, This is my first contribution, so I apologize in advance if this is the wrong place. I also agree that this property should be added. Especially because it maps to a metadata from the Minimal Information about any sequences (MIxS) described [1]https://genomicsstandardsconsortium.github.io/mixs/0000015/ and with the following authorized values: [2]https://genomicsstandardsconsortium.github.io/mixs/RelToOxygenEnum/.
- That being said, the values can all be mapped back to the Ontology of Prokaryotic Phenotypic and Metabolic Characters [3]https://www.ebi.ac.uk/ols/ontologies/micro
- Example:
- Anaerobic Q189790: anaerobe [4]http://purl.obolibrary.org/obo/MICRO_0001517
- Microaerobe Q548321: microaerobe [5]http://purl.obolibrary.org/obo/MICRO_0001515
- Best,
- Charlie Lhippovert (talk) 13:55, 30 January 2023 (UTC)
- Discussion
Salinity
Is not yet possible with the WD properties
Currently there are 4 types of adaptations described for lower and higher organisms (mostly fish like)
Property | Label | Data type | Expected value |
---|---|---|---|
Unknown | Salinity type | item | Euryhaline Q2630188
Halophile Q946633 Halotolerance Q1529024 Stenohaline Q2853549 |
pH
Is not yet possible with the WD properties
Definition of the range of the pH Q40936 for a given organism.
Property | Label | Data type | Expected value |
---|---|---|---|
Unknown | pH optimum | item | Optimal pH for organism under normal conditions |
Unknown | pH minimum | item | Minimum pH for organism under normal conditions |
Unknown | pH maximum | item | Maximum pH for organism under normal conditions |
Geographical location
There is information available at certain levels. Sometimes there is country information, continental information and sometimes there are GPS coordinates. I'll post a snapshot soon of how this information looks like.