Wikidata:WikiProject Microbiology/Properties/pl

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This page is a translated version of the page Wikidata:WikiProject Microbiology/Properties and the translation is 2% complete.

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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 ...

Property Label Data type Expected value
Property: P1604 biosafety level item Level 1 Q18396533

Level 2 Q18396535

Level 3 Q18396538

Level 4

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

Documentation

The ID "WikiProject Microbiology/Properties" is unknown to the system. Please use a valid entity ID.

[create] Create a translatable help page (preferably in English) for this property to be included here

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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)

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.