Wikidata:WikiProject Microbiology/Properties/pl

Properties accepted

Gram staining

Property:P2597

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

   Under discussion

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.