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2018 Berkeley GO-Dev July Hackathon

GO wiki (new pages) - Wed, 07/11/2018 - 10:32

Debert: Created page with "== Dates == July 19-20 == Location == LBL Potter Street ??? http://berkeleybop.org/team_contact Rooms: ??? == Agenda == Potential topics: * GO to PAINT monthly update pro..."

== Dates ==

July 19-20

== Location ==

LBL Potter Street ???
http://berkeleybop.org/team_contact

Rooms:
???

== Agenda ==
Potential topics:
* GO to PAINT monthly update process - [https://github.com/pantherdb/fullgo_paint_update repo here]

== Attendees ==
[https://docs.google.com/spreadsheets/d/1yNbXfktsDs_hI0lNv57aYa7XbPlCiwFvYp5ZqDGuTZM/edit?ts=5b201484#gid=0 Google sheet]
* LBL GO-dev team
* Dustin (USC)
* Paul (USC)
* Huaiyu (USC)
* Anushya (USC)
* Tremayne (remote)

[[Category:Meetings]] Debert
Categories: GO Internal

Biological Pathways as GO-CAMs

GO wiki (new pages) - Tue, 07/10/2018 - 09:30

Ben.good: Opening documentation page for pathways to GO project.



==Mapping from Reactome pathways to GO-CAM models==
* gdoc https://docs.google.com/document/d/1xKr4sMBMioEYnHFpnFl0lL2gQzpeHX-eY3wT0fyZXEA/edit#
* presentation https://docs.google.com/presentation/d/1T6QmR7MeXWH6Q3hMgpp-A09zDwTUplWcrVSZRhS_InU/edit#slide=id.p3
* code

==Alignment between RHEA, Reactome, and GO==
Once a pathway is converted into the OWL structure of a GO-CAM, OWL reasoners such as [https://github.com/balhoff/arachne|Arachne] and [https://github.com/liveontologies/elk-reasoner|ELK] can be applied to infer class membership for component reactions (as GO molecular functions) and pathways (as biological processes). Classifying the members of GO-CAM models with the GO makes it possible to query the integrated knowledge base using the structure of the GO. For example, queries like 'show all genes involved in Wnt signaling' can leverage the knowledge in pathway databases (e.g., the [https://reactome.org/PathwayBrowser/#/R-HSA-3858494&SEL=R-HSA-4086400&PATH=R-HSA-162582,R-HSA-195721|PCP/CE Wnt pathway from Reactome]) but query using GO terms (e.g., [https://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0060071|Wnt signaling pathway, planar cell polarity pathway GO:0060071] and its parent [https://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0016055|Wnt signaling pathway GO:0016055]).

In this example, Reactome curators have already provided the mapping to GO classes, but this is not always the case. Within Reactome, which is one of the most intensely manually curated pathway knowledge bases with the deepest connections to the GO, only about 50% of the reactions and 50% of the pathways are mapped to GO terms. In many other databases, e.g., many of those collected in the Pathway Commons collection, there are no mappings at all. Apart from manually adding these classifications (a solution that has problems with cost, consistency and scale), it is possible to infer them automatically based on logical definitions (written as OWL axioms) for GO terms. While there are many such definitions, there are large gaps in areas of importance to pathways such as Catalytic Activity and Binding.

The goal of this project is to leverage the RHEA database of biochemical reactions to construct logical definitions for the children of Catalytic Activity. This should help automate the classification of Pathway components, thus facilitating integration into the GO-CAM knowledge base. Further, it should help improve the structure of this branch of the GO. The project is being tracked in the [https://github.com/geneontology/go-ontology/projects/10|GitHub project GO-Reactome-Rhea alignment]

===Logically defining Catalytic Activity===
The definitions are structured primarily based on the inputs and outputs of the reaction. For example, a logical definition for the GO term ‘nucleoside phosphate kinase activity’ amounts to the rule:
If
X has type 'catalytic activity'
and X has input ATP and X has input nucleoside 5'-monophosphate
and X has output ADP and X has output nucleoside 5'-diphosphate
Then
X has type nucleoside phosphate kinase activity'

This definition can be extracted automatically from the [https://www.rhea-db.org/reaction.xhtml?id=24039|RHEA database entry] which is an xref of the GO term nucleoside phosphate kinase activity.

===Results===

===Code===

[[Category:GO-CAM]]
[[Category:ontology]]
[[Category:Documentation]]
[[Category:Reasoning]]
[[Category:Research]] Ben.good
Categories: GO Internal

Annotation Conf. Call 2018-07-10

GO wiki (new pages) - Mon, 07/09/2018 - 17:32

Vanaukenk:

= Meeting URL =
*https://stanford.zoom.us/j/976175422

== GO Conference Calls ==
=== Tuesdays ===
*Still will be Tuesdays at 8am PDT
*Proposed meeting schedule:
**1st Tuesday: Alliance Gene Function
**2nd Tuesday: GO Consortium
**3rd Tuesday: Alliance Gene Function/GO-CAM Working Group
**4th Tuesday: GO-CAM Working Group
**5th Tuesday: ad hoc, as needed
*One Zoom URL for all - https://stanford.zoom.us/j/976175422

=== Wednesdays ===
*Wednesday Noctua call technical call is suspended for the time being
*The software team will be discussing infrastructure and other development issues on their go-dev calls
*When needed, curators will be asked for feedback on Noctua features

== Curation Guidelines ==
=== Annotation of Transmembrane Proteins ===
*[http://wiki.geneontology.org/index.php/Transmembrane_Proteins Guidelines for Annotating Transmembrane Proteins]

=== Transcription Factors ===


[[Category:Annotation Working Group]] Vanaukenk
Categories: GO Internal

Ontology meeting 2018-07-09

GO wiki (new pages) - Fri, 07/06/2018 - 05:36

David: Created page with "= Conference Line = *Zoom: https://stanford.zoom.us/j/828418143 = Agenda = == Editors Discussion == ===Project Update=== ====Reactome-Rhea-GO Alignment----https://github.c..."

= Conference Line =

*Zoom: https://stanford.zoom.us/j/828418143

= Agenda =

== Editors Discussion ==

===Project Update===
====Reactome-Rhea-GO Alignment----https://github.com/geneontology/go-ontology/projects/10====
====ECM Project--- https://github.com/geneontology/go-ontology/projects/9====

=== Regenerate Imports File ===
Docker has worked successfully for regenerating the CL import and appears to have worked for the ChEBI import.

We will continue to test this for a little while longer and then train all editors in the procedure.

=== Obsoletion plugin for Protege ===
Kimberly and presumably Pascale need to update their plugins. If there are issues, can you contact Jim for help?

=== Ontology Documentation ===
Nothing last week, too busy. We will resume again tomorrow.

===Ontology Developers' workshop possibility===
* Now completely up in the air. November in Denver, December in Geneva?? We need to have a concrete agenda.

==GH project link==
https://github.com/geneontology/go-ontology/projects/1

= Minutes =
*On call:


[[Category: Ontology]]
[[Category: Meetings]] David
Categories: GO Internal

Transport and transporters

GO wiki (new pages) - Tue, 07/03/2018 - 07:32

Pascale:

TO DO: compare to http://wiki.geneontology.org/index.php/Transporter_terms_standard_definitions

=Process: Transport and Localization=
This area of the biological process ontology covers the processes involved in positioning a substance or cellular entity and maintaining it in that location.
Terms and Structure

The processes that influence the location of a substance or entity in or outside the cell fall under the general term localization. Localization is split into two parts; there is the establishment of localization, which covers transport and/or autonomous movement of substances or cellular components, as well as orienting a protein or organelle. The maintenance of localization covers sequestering and active retrieval processes.

The structure to represent the localization of a substance or entity is shown below.

x localization
[p] establishment of x localization
[i] establishment of x orientation
[i] x movement
[i] x transport
[i] x export
[i] x import
[i] x secretion
[p] maintenance of x localization
[i] sequestering of x

=Standard Definitions=
Note that not all localization terms have standard definitions at present; as a guide to term usage, x movement should be used to refer to the change in position of entities that can propel themselves, whilst x intended for substances that are moved by another entity. Storage, retention or sequestration are represented by the term sequestering of x.

*'''x localization''': The processes by which x (where x is a substance or cellular entity, such as a protein complex or organelle) is transported to, and maintained in, a specific location.
*'''establishment of x localization''': The directed movement of x to a specific location.
*'''maintenance of x localization''': The processes by which x is maintained in a location and prevented from moving elsewhere.
*'''x secretion''': The regulated release of x from a cell or group of cells.
*'''x transport''': The directed movement of x into, out of or within a cell, or between cells.
*'''x export''': The directed movement of x out of a cell or organelle.
*'''x import''': The directed movement of x into a cell or organelle.
*'''establishment of x orientation''': The processes that set the alignment of x relative to other cellular structures.

=Function: Transporter activity=
==Terms and Structure==

[i]transmembrane transporter activity
[i]active transporter activity
[i]primary active transporter activity
[i]decarboxylation-driven active transporter activity
[i]light-driven active transporter activity
[i]methyl transfer-driven active transporter activity
[i]oxidoreduction-driven active transporter activity
[i]P-P-bond-hydrolysis-driven transporter activity
[i]secondary active transporter activity
[i]antiporter activity
[i]symporter activity
[i]uniporter activity

[i]transmembrane transporter activity
[i]passive transmembrane transporter activity
[i]channel activity
[i]gated channel activity
[i]dephosphorylation-gated channel activity
[i]ion gated channel activity
[i]ligand-gated channel activity
[i]mechanically gated channel activity
[i]phosphorylation-gated channel activity
[i]voltage-gated channel activity

[i]transporter activity
[i]substrate-specific transporter activity
[i]substrate-specific transmembrane transporter activity
[i]transmembrane transporter activity
[i]substrate-specific transmembrane transporter activity

[i]transmembrane transporter activity
[i]efflux transmembrane transporter activity
[i]uptake transmembrane transporter activity

=Transporter Standard Definitions=
==Active Transporters==

*'''X transmembrane transporter activity''': Catalysis of the transfer of X from one side of the membrane to the other. X is [insert description].
*'''X uptake transmembrane transporter activity''': Catalysis of the transfer of X from the outside of a cell to the inside of a cell across a membrane. X is [insert description].
*'''X efflux transmembrane transporter activity''': Catalysis of the transfer of X from the inside of a cell to the outside of the cell across a membrane. X is [insert description].
*'''active transmembrane X transporter activity''': Catalysis of the transfer of X from one side of the membrane to the other, up the solute's concentration gradient. The transporter binds the solute and undergoes a series of conformational changes. Transport works equally well in either direction. X is [insert description].
*'''primary active transmembrane X transporter activity''': Catalysis of the transport of X across a membrane, up the solute's concentration gradient, by binding the solute and undergoing a series of conformational changes. Transport works equally well in either direction and is driven by a primary energy source. Primary energy sources known to be coupled to transport are chemical, electrical and solar sources. X is [insert description].
*'''decarboxylation-driven active transmembrane X transporter activity''': Enables the transport of X across a membrane, up the solute's concentration gradient, by binding the solute and undergoing a series of conformational changes. Transport works equally well in either direction and is driven by decarboxylation of a cytoplasmic substrate. X is [insert description].
*'''light-driven active transmembrane X transporter activity''': Enables the transport of X across a membrane, up the solute's concentration gradient, by binding the solute and undergoing a series of conformational changes. Transport works equally well in either direction and is driven by light. X is [insert description].
*'''methyl transfer-driven active transmembrane X transporter activity''': Enables the transport of X across a membrane, up the solute's concentration gradient, by binding the solute and undergoing a series of conformational changes. Transport works equally well in either direction and is driven by a methyl transfer reaction. X is [insert description].
*'''oxidoreduction-driven active transmembrane X transporter activity''': Enables the transport of X across a membrane, up the solute's concentration gradient, by binding the solute and undergoing a series of conformational changes. Transport works equally well in either direction and is driven by an exothermic flow of electrons from a reduced substrate to an oxidized substrate. X is [insert description].
*'''P-P-bond-hydrolysis-driven transmembrane X transporter activity''': Enables the transport of X across a membrane, up the solute's concentration gradient, by binding the solute and undergoing a series of conformational changes. Transport works equally well in either direction and is driven by the hydrolysis of the diphosphate bond of inorganic pyrophosphate, ATP, or another nucleoside triphosphate. The transport protein may or may not be transiently phosphorylated, but the substrate is not phosphorylated. X is [insert description].
*'''secondary active transmembrane X transporter activity''': Catalysis of the transfer of X from one side of the membrane to the other, up the solute's concentration gradient. The transporter binds the solute and undergoes a series of conformational changes. Transport works equally well in either direction and is driven by a chemiosmotic source of energy. Chemiosmotic sources of energy include uniport, symport or antiport. X is [insert description].
*'''X:solute antiporter activity''': Catalysis of the transfer of X from one side of the membrane to the other, up the solute's concentration gradient. The transporter binds the solute and undergoes a series of conformational changes. Transport works equally well in either direction and is driven by a antiport mechanism whereby two or more species are transported in opposite directions in a tightly coupled process not directly linked to a form of energy other than chemiosmotic energy. X is [insert description].
*'''X:solute symporter activity''': Catalysis of the transfer of X from one side of the membrane to the other, up the solute's concentration gradient. The transporter binds the solute and undergoes a series of conformational changes. Transport works equally well in either direction and is driven by a symport mechanism whereby two or more species are transported together in the same direction in a tightly coupled process not directly linked to a form of energy other than chemiosmotic energy. X is [insert description].
*'''X uniporter activity''': Catalysis of the transfer of X from one side of the membrane to the other, up the solute's concentration gradient. The transporter binds the solute and undergoes a series of conformational changes. Transport works equally well in either direction and is driven by a uniport mechanism which is independent of the movement of any other molecular species. X is [insert description].

In secondary active transporter defs include a reaction where possible. For example:

Catalysis of the reaction: sugar(out) + H+(out) = sugar(in) + H+(in). Catalysis of the reaction: solute(out) + H+(out) = solute(in) + H+(in).

=Passive Transporters=

*'''passive transmembrane X transporter activity''': Catalysis of the transfer of X from one side of the membrane to the other, down the solute's concentration gradient. X is [insert description].
*'''X channel activity''': Catalysis of facilitated diffusion of X (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism.
*'''gated X channel activity''': Catalysis of the transmembrane transfer of X by a channel that opens in response to a specific stimulus.
*'''dephosphorylation-gated X channel activity''': Catalysis of the transmembrane transfer of X by a channel that opens in response to dephosphorylation of one of its constituent parts.
ion-gated X channel activity''': Catalysis of the transmembrane transfer of X by a channel that opens in response to a specific ion stimulus.
*'''ligand-gated X channel activity''': Catalysis of the transmembrane transfer of X by a channel that opens when a specific ligand has been bound by the channel complex or one of its constituent parts.
*'''mechanically-gated X channel activity''': Catalysis of the transmembrane transfer of X by a channel that opens in response to a mechanical stress.
phosphorylation-gated X channel activity''': Catalysis of the transmembrane transfer of X by a channel that opens in response to phosphorylation of one of its constituent parts.
*'''voltage-gated X channel activity''': Catalysis of the transmembrane transfer of X by a channel whose open state is dependent on the voltage across the membrane in which it is embedded.
*'''X channel activity''': Catalysis of facilitated diffusion of X (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism.
*'''x gated y channel activity''': Catalysis of the transmembrane transfer of y by a channel that opens in response to stimulus by x. Transport by a channel involves catalysis of facilitated diffusion of a solute (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel, without evidence for a carrier-mediated mechanism.

=Other standard definitions=

*'''L-amino acid''': L-Y is the levorotatory isomer of [insert systematic name].
*'''D-amino acid''': D-Y is the dextrorotatory isomer of [insert systematic name].
*'''constitutive activity''': This activity is constitutive and therfore always present, regardless of demand.
*'''inducible activity''': This activity is inducible and therefore only present when there is demand.
*'''high affinity''': In high affinity transport the transporter is able to bind the solute even if it is only present at very low concentrations.
*'''low affinity''': In low affinity transport the transporter is able to bind the solute only if it is present at very high concentrations.


----
[[Category:GO Editors]][[Category:Ontology]]
[[Notes_on_specific_terms |Back to: Notes on specific terms]] Pascale
Categories: GO Internal

Sensory perception

GO wiki (new pages) - Tue, 07/03/2018 - 07:25

Pascale: Created page with "=Terms and Structure= Sensory perception occurs in organisms capable of performing neurophysiological processing of the stimuli in their environment, and covers the processes..."

=Terms and Structure=

Sensory perception occurs in organisms capable of performing neurophysiological processing of the stimuli in their environment, and covers the processes commonly called "the senses": hearing, vision, taste, smell and so on. Sensory perception involves detection of the stimulus and subsequent recognition and characterization of it. There are five different stimulus types involved in sensory processing - chemical, mechanical, electrical, light and temperature.

neurophysiological process
[i] sensory perception
[p] detection of stimulus during sensory perception
[i] detection of chemical stimulus during sensory perception
[i] detection of electrical stimulus during sensory perception
[etc.]
[i] sensory perception of chemical stimulus
[p] detection of chemical stimulus during sensory perception
[i] sensory perception of electrical stimulus
[p] detection of electrical stimulus during sensory perception
[etc.]

The (known) senses are represented as processes underneath sensory perception. Most are worded sensory perception of [stimulus modality], e.g. sensory perception of sound, sensory perception of touch, although some have more common names, such as visual perception or electroception.

A combination of stimuli may be used by some of the senses; for example, sensory perception of pain may come from temperature, mechanical, electrical or chemical stimuli. Similarly, stimuli of a certain type may be perceived by different senses: e.g. both sense of smell and taste use chemical stimuli. The structure is as follows:

sensory perception
[i] sensory perception of chemical stimulus
[i] sensory perception of smell
[p] detection of chemical stimulus during sensory perception of smell
[i] sensory perception of taste
[p] detection of chemical stimulus during sensory perception of taste
[p] detection of chemical stimulus during sensory perception
[i] detection of chemical stimulus during sensory perception of smell
[i] detection of chemical stimulus during sensory perception of taste
[i] detection of chemical stimulus during sensory perception of pain

...

[i] sensory perception of pain
[p] detection of chemical stimulus during sensory perception of pain
[p] detection of electrical stimulus during sensory perception of pain
[p] detection of mechanical stimulus during sensory perception of pain
[p] detection of temperature stimulus during sensory perception of pain

This structure is also repeated under the response to stimulus node:

response to stimulus
[i] detection of stimulus
[i] detection of chemical stimulus
[i] detection of chemical stimulus during sensory perception
[i] detection of chemical stimulus during sensory perception of smell
[i] detection of chemical stimulus during sensory perception of taste
[i] detection of stimulus during sensory perception
[i] detection of chemical stimulus during sensory perception

...

[i] sensory perception
[p] detection of stimulus during sensory perception
[i] detection of chemical stimulus during sensory perception
[etc.]

sensory perception of xxx may have the exact synonym perception of xxx.

=Standard Definitions=

*'''sensory perception:''' The series of events required for an organism to receive a sensory stimulus, convert it to a molecular signal, and recognize and characterize the signal.
*'''sensory perception of [stimulus type] stimulus:''' The series of events required for an organism to receive a [stimulus type] stimulus, convert it to a molecular signal, and recognize and characterize the signal.
*'''detection of [stimulus type] stimulus during sensory perception of [sensory modality]:''' The series of events during the perception of [sensory modality] in which a [stimulus type] stimulus is received and converted to a molecular signal.




----
[[Category:GO Editors]][[Category:Ontology]]
[[Notes_on_specific_terms |Back to: Notes on specific terms]] Pascale
Categories: GO Internal

Detection and Response to stimulus

GO wiki (new pages) - Tue, 07/03/2018 - 07:23

Pascale:

=Terms and Structure=
The response of a cell or an organism to a stimulus is all the processes that occur as a result of the stimulus occurring within or outside the cell or organism. Detection of the stimulus, the process in which a stimulus is received by a cell and converted into a molecular signal, is thus a class of stimulus response. The general structure of this node is as follows:

response to stimulus
[i] detection of stimulus
[i] detection of [stimulus type] stimulus
[i] response to [stimulus type] stimulus
[i] detection of [stimulus type] stimulus
[i] [examples of processes which occur in response to [stimulus type] stimulus]

There may be different types of response to a stimulus, such as cellular or behavioral responses. The structure for these terms would be:

response to [stimulus type] stimulus
[i] behavioral response to [stimulus type] stimulus
[i] cellular response to [stimulus type] stimulus

Note that sensory perception is a special class of response to stimulus; please see the [[Sensory_perception sensory perception documentation]]. The phrase perception of xxx should only be used in names or definitions of terms relevant to organisms capable of performing neural processing of the signal generated by the stimulus, but xxx sensing is considered by GO to be synonymous with detection of xxx.

=Standard Definitions=

* '''response to [stimulus type] stimulus:''' A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a [stimulus type] stimulus.
* '''cellular response to [stimulus type] stimulus:''' A change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a [stimulus type] stimulus.
* '''behavioral response to [stimulus type] stimulus:''' A change in the behavior of an organism as a result of a [stimulus type] stimulus.
* '''age-dependent response to [stimulus type] stimulus:''' A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a [stimulus type] stimulus, where the change varies according to the age of the cell or organism.
*'''detection of [stimulus type] stimulus:''' The series of events in which a chemical stimulus is received and converted into a molecular signal.


----
[[Category:GO Editors]][[Category:Ontology]]
[[Notes_on_specific_terms |Back to: Notes on specific terms]] Pascale
Categories: GO Internal

Other Organisms and Viruses

GO wiki (new pages) - Tue, 07/03/2018 - 07:16

Pascale:

=Multi-Organism Process=

Multi-organism process and its children were created in Jan 2005 in collaboration with the Plant-Associated Microbe GO interest group (PAMGO) to describe interactions that occur between organisms of different species, and to subsume the existing terms that described interactions between organisms, e.g. pathogenesis and host-pathogen interaction. These terms were felt to be too 'host-centric', due to their reference to the disease process and their non-systematic placement in the ontologies. Further terms were added after the November 2005 content meeting to flesh out the node further.

Complementary terms exist for annotating cellular locations such as host cell nucleus; see the cellular component guidelines for more details. The GO annotation conventions have a guide to annotating with these terms and how to represent the other organism in the interaction.

=Terms and structure=

Multi-organism processes are categorized according to the nature of the interaction (behavioral or physiological), and by whether they are inter- or intra-species. Interspecies interactions of an intimate or co-dependent nature fall under the term symbiosis, encompassing mutualism through parasitism, which covers all types of symbiosis between species, including mutualism (where the association is advantageous to one, or usually both, organisms) and parasitism (where the association is advantageous to one organism but detrimental to the other). All new terms that describe interactions between organisms should be placed in the interaction between organisms node under the appropriate parent(s).

The node is structured broadly like this (not all terms shown):

multi-organism process
[i] interspecies interaction between organisms
---[i] symbiosis, encompassing mutualism through parasitism
[i] intraspecies interaction between organisms

Symbiotic relationships may be between two organisms of similar sizes or of differing sizes, and most of the processes under symbiosis, encompassing mutualism through parasitism have child terms to specify the sizes of the organisms involved. These terms use the nomenclature host for the larger organism and symbiont for the smaller organism. For interactions where there is no clear host or symbiont, the wording other organism is used, and terms are appended with during symbiotic interaction to make it clear that they represent processes occurring during symbiosis.

symbiosis, encompassing mutualism through parasitism
[i] acquisition of nutrients from other organism during symbiotic interaction
---[i] acquisition of nutrients from host
---[i] acquisition of nutrients from symbiont
[i] interaction with host
---[i] acquisition of nutrients from host
[i] interaction with symbiont
---[i] acquisition of nutrients from symbiont

Some processes may occur as part of symbiosis or outside it; the structure to represent such a process is illustrated below. Note that terms representing non-symbiotic interactions between organisms should use the wording another organism to refer to the second organism.

interaction between organisms
[i] physiological interaction between organisms
---[i] killing of cells of another organism
------[i] killing of cells of other organism during symbiotic interaction
---------[i] killing of host cells
---------[i] killing of symbiont cells
[i] interspecies interaction between organisms
---[i] symbiosis, encompassing mutualism through parasitism
------[i] killing of cells of other organism during symbiotic interaction
---------[i] killing of host cells
---------[i] killing of symbiont cells

=Standard Definitions=

*'''[process involving] other organism during symbiotic interaction''': [definition of process], where the two organisms are in a symbiotic relationship.

*'''[process involving] host''': [definition of process]. The host is defined as the larger of the organisms involved in a symbiotic interaction.

*'''[process involving] symbiont''': [definition of process]. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction.

Taking the process acquisition of nutrients as an example, the terms and definitions would be as follows:

*'''acquisition of nutrients from other organism during symbiotic interaction''': The production of structures and/or molecules in an organism that are required for the acquisition and/or utilization of nutrients obtained from a second organism, where the two organisms are in a symbiotic relationship.
*'''acquisition of nutrients from host''': The production of structures and/or molecules in an organism that are required for the acquisition and/or utilization of nutrients obtained from its host. The host is defined as the larger of the organisms involved in a symbiotic interaction.
*'''acquisition of nutrients from symbiont''': The production of structures and/or molecules in an organism that are required for the acquisition and/or utilization of nutrients obtained from its symbiont. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction.

=Hosts, Symbionts and Viruses=

The cellular component ontology provides terms to complement those in the biological process ontology representing multi-organism processes. There are two main locations for these terms: the first set, for the representation of the larger organism in the interaction, can be found under host in extraorganismal space; the second set are to capture virus components, and are under the term virion.

cellular_component
[i] extracellular region
---[p] extracellular region part
------[i] extraorganismal space
---------[i] host
...
[i] virion

Viruses should be annotated like any other organism involved in a multi-organism process, using cellular component terms such as host cell cytoplasm or host cell nucleus. Locations in the virus itself are found under the term virion.



The GO annotation conventions have a guide to annotating with these terms and how to represent the other organism in the interaction. '''DOES THAT STILL EXIST ?'''



----
[[Category:GO Editors]][[Category:Ontology]]
[[Notes_on_specific_terms |Back to: Notes on specific terms]] Pascale
Categories: GO Internal

Membrane proteins

GO wiki (new pages) - Tue, 07/03/2018 - 06:48

Pascale:

As GO cellular component terms describe locations where a gene product may act, rather than physical features of proteins or RNAs, the terms integral membrane protein and peripheral membrane protein are present only as non-exact synonyms. GO distinguishes classes of membrane-related location:

* '''extrinsic component of membrane ; GO:0019898''' refers to gene products that are associated with membranes, but are neither directly embedded in the membrane nor anchored by covalent bonds to any moiety embedded in the membrane.

* '''intrinsic component of membrane ; GO:0031224''' refers to gene products that have some covalently attached moiety embedded in the membrane, and is further split into integral component of membrane ; GO:0016021 and anchored component of membrane ; GO:0031225. The former refers to proteins in which some part of the peptide sequence spans all or part of the membrane (in theory, it could also be used for RNAs embedded in a membrane, if any such exist). A subclass of this covers transmembrane proteins - those that completely span the membrane (see examples in figure 2). The latter refers to gene products tethered to a membrane by a covalently attached anchor, such as a lipid moiety, which is embedded in the membrane.

Each of these terms can have child terms referring to specific membranes, for example intrinsic component of plasma membrane ; GO:0031226 or extrinsic component of vacuolar membrane ; GO:0000306.

Additionally, monotopic (non-membrane spanning proteins, as illustrated in figure 3) can be assigned to a side of membrane : "A cellular component consisting of one leaflet of a membrane bilayer and any proteins embedded or anchored in it or attached to its surface." As for whole membranes, proteins can be more specifically annotated as integral (Fig 3. 1 & 2), anchored (Fig 3. 3) or extrinsic components (Fig 3. 4) of a side of membrane.


[[Image:Diag-membrane.gif]]

'''Figure 1: Membrane component types.'''


[[Image:Polytopic membrane protein.png]]


'''Figure 2: Polytopic proteins. '''Schematic representation of transmembrane proteins: 1. a single transmembrane α-helix (bitopic membrane protein) 2. a polytopic transmembrane α-helical protein 3. a polytopic transmembrane β-sheet protein. The membrane is represented in light-brown. Source for image and legend: Wikipedia. See link for image credit.

[[Image:Monotopic membrane protein.png]]


'''Figure 3: Monotopic proteins. '''Schematic representation of the different types of interaction between monotopic membrane proteins and the cell membrane: 1. interaction by an amphipathic α-helix parallel to the membrane plane (in-plane membrane helix) 2. interaction by a hydrophobic loop 3. interaction by a covalently bound membrane lipid (lipidation) 4. electrostatic or ionic interactions with membrane lipids (e.g. through a calcium ion). Source for image and legend: Wikipedia. See link for image credit.

Unsupported assertions about membrane proteins

The cellular component ontology does not include terms for type I, II, etc., membrane proteins, because these classifications are not locations, but instead describe a different feature of the proteins, namely topological orientation with respect to the membrane and other cellular components. Furthermore, the wording "type I integral membrane protein" describes a class of gene products.
Definition patterns

extrinsic component of X membrane: "The component of the X membrane consisting of gene products that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region."

intrinsic component of X membrane: "The component of the X membrane consisting of gene products and protein complexes that have some covalently attached part (e.g. peptide sequence or GPI anchor), which spans or is embedded in one or both leaflets the membrane."

integral component of X membrane: "The component of the X membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane."

anchored component of X membrane: "The component of the X membrane consisting of the gene products and protein complexes that are tethered to the membrane only by a covalently attached anchor, such as a lipid group embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping."

spanning component of X membrane "The component of the X membrane consisting of gene products and protein complexes that have some part that spans both leaflets of the membrane."

X side of Y membrane: "The side (leaflet) of the X that faces the Y."

extrinsic component of X side of Y membrane: "The component of the Y membrane consisting of gene products and protein complexes that are loosely bound to its X surface, but not integrated into the hydrophobic region."

intrinsic component of X side of Y membrane: "The component of the X membrane consisting of gene products and protein complexes that penetrate the Y side of the membrane only, either directly or via some covalently attached hydrophobic anchor."
Ontology structure

Using plasma membrane as an example, each membrane has intrinsic and extrinsic components:
intrinsic_vs_extrinsic_membrane_comp_0.png

Each membrane has 2 sides - in this case cytoplasmic and external, each with their own intrinsic and extrinsic components:
sides_of_pm_0.png

Intrinsic and extrinsic components of the sides are subclasses (is_a children) of the corresponding terms for the whole membrane:
side_of_mem_and_in_vs_ex_0.png
Logical definitions
side of membrane terms

We have general classes for cytoplasmic and lumenal membrane sides, defined using adjacent to, e.g.

'cytoplasmic side of membrane' EquivalentTo 'side of membrane' that adjacent_to some cytoplasm

This general pattern is sufficient for classification of side of membrane terms:

'side of membrane' that (part_of some X) and (adjacent_to some Y)

For example, this allows inferred classification as 'early endosome membrane part' and 'cytoplasmic side of membrane':

'cytoplasmic side of early endosome membrane' EquivalentTo: 'side of membrane' that (part_of some 'early endosome membrane') and (adjacent_to some cytoplasm)"

extrinsic, intrinsic, integral and anchored components

'X component' that part_of some 'Y membrane/side of membrane' e.g.:

'integral component of membrane' that (part_of some 'Golgi membrane')

'integral component of membrane' that (part_of some 'lumenal side of endoplasmic reticulum membrane')

These patterns automate classification, but part_of relationships (see plasma membrane example above for a guide) still need to be added by hand. This could be automated in future by the use of GCIs in OWL, but these are rather ungainly to roll by hand and so will probably be added via templates following these patterns, or via some script-based support mechanism.


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[[Category:GO Editors]][[Category:Ontology]]
[[Notes_on_specific_terms |Back to: Notes on specific terms]] Pascale
Categories: GO Internal

Development

GO wiki (new pages) - Tue, 07/03/2018 - 06:12

Pascale: /* B. Seed Maturation */

The set of standard terms below can be applied to each developing structure in each species covered in the ontology. However it is generally not practical to implement every term for every structure, since this would lead to a massive proliferation of terms. Where one term e.g. x development, is present, the rest of the terms for the development of x are considered to be implied, without having actually been implemented. Further terms are generally only implemented when they are required for annotation. To see an example of a more full implementation please see the children of mesoderm development, which cover the development of the mesoderm, and the axial, paraxial, and intermediate mesoderm.

This development node structure was agreed upon in 2003 and is gradually being retrofitted. Where terms appear not to conform to it, this may be because they have not yet been retrofitted, or because their development includes an exception to the normal model.

=Terms and Structure=

This is the structure for development terms involving tissues, organs and organisms (based on those SourceForge discussions: https://sourceforge.net/p/geneontology/ontology-requests/1235/ and https://sourceforge.net/p/geneontology/ontology-requests/1242/).

x development
[p]z cell differentiation (where z is a cell that is part_of x)
[p] x morphogenesis
[p] x formation
[p] y cell differentiation (where y is a cell of the primordial structure)
[p] x structural organization
[p] x maturation

This is the structure for development terms involving cells (agreed at the [http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/meeting/minutes/20030125_StCroix.txt?rev=1.1;content-type=text%2Fplain 2003 St. Croix consortium meeting]).

cellular process
[i] cell differentiation
[p] cell fate commitment
[p] cell fate specification
[p] cell fate determination
[p] cell development
[p] cellular morphogenesis during differentiation
[p] cell maturation

=Standard Definitions=

On implementation, each of the standard definitions below should be followed by a brief summary of the purpose of the structure, and also, where relevant, the characteristics marking its initial formation and its arrival at the mature state. If the common usage does not conform to GO term name syntax, then it is helpful to add an exact synonym with GO syntax.

* '''x development:''' The process whose specific outcome is the progression of the x over time, from its formation to the mature structure.
* '''x morphogenesis:''' The process in which the anatomical structures of x are generated and organized.
* '''x formation:''' The process that gives rise to x. This process pertains to the initial formation of a structure from unspecified parts.
* '''x structural organization:''' The process that contributes to creating the structural organization of x. This process pertains to the physical shaping of a rudimentary structure.
* '''x maturation:''' A developmental process, independent of morphogenetic (shape) change, that is required for x to attain its fully functional state. [description of x]
* '''[cell type] cell differentiation:''' The process whereby a relatively unspecialized cell acquires specialized features of a [cell type] cell. (N.B. This may be development of [cell type] cell type or a set of cells of [cell type] cell type. This will involve the change of a cell or set of cells from one cell identity to another.)
* '''[cell type] cell fate commitment:''' The process whereby the developmental fate of a cell becomes restricted such that it will develop into a [cell type] cell.
* '''[cell type] cell fate specification:''' The process whereby a cell becomes capable of differentiating autonomously into a [cell type] cell in an environment that is neutral with respect to the developmental pathway. Upon specification, the cell fate can be reversed.
* '''[cell type] cell fate determination:''' The process whereby a cell becomes capable of differentiating autonomously into a [cell type] cell regardless of its environment; upon determination, the cell fate cannot be reversed.
* '''[cell type] cell development:''' The process aimed at the progression of a [cell type] cell over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell.
* '''[cell type] cell morphogenesis during differentiation:''' The process in which the structures of a [cell type] cell are generated and organized. This process occurs while the initially relatively unspecialized cell is acquiring the specialized features of a [cell type] cell.
* '''[cell type] cell maturation:''' A developmental process, independent of morphogenetic (shape) change, that is required for a [cell type] cell to attain its fully functional state. [description of [cell type]]
* '''Note: See Other Miscellaneous Standard Defs below for x biogenesis.'''

=Qualifiers=

The following qualifiers can be used with morphogenesis.

embryonic x morphogenesis
The process, occurring in the embryo, by which the anatomical structures of x are generated and organized.
larval x morphogenesis
The process, occurring in the larva, by which the anatomical structures of x are generated and organized.
post-embryonic x morphogenesis
The process, occurring after embryonic development [and prior to (e.g. larval) development], by which the anatomical structures of x are generated and organized.

=Development vs Morphogenesis=

The concepts of development and morphogenesis may at first seem synonymous. On further thought however, it becomes apparent that at the level of tissues, organs and organisms, development encompasses much more than just the generation and organization of anatomical structures. In some instances it includes steps called maturation which may include a wide range of processes, one of which is described below.

=Seed development=

Seeds are complex structures whose development includes both a morphogenesis and maturation step (this [https://sourceforge.net/p/geneontology/ontology-requests/1600/ SourceForge discussion]).

==A. Seed Morphogenesis==

The morphogenesis phase includes generation and organization steps, as described in Developmental Biology, 6th Edition (Scott F. Gilbert):
* To establish the basic body plan. Radial patterning produces three tissue systems, and axial patterning establishes the apical-basal (shoot-root) axis.
* To set aside meristematic tissue for postembryonic elaboration of the body structure (leaves, roots, flowers, etc.).
* To establish an accessible food reserve for the germinating embryo until it becomes autotrophic.

==B. Seed Maturation==

In many species the fully formed seed enters a physiological state of dormancy, and this is an example of a maturation process. At this point morphogenesis is over, but development continues with onset of dormancy phase.

[[Image:Diag-seed-dormancy.gif]]

=Formation vs Development=

Confusion often arises about the role of formation in the development process. Formation would have to do with the processes that establish a tissue. A couple of examples of these would be primary embryonic induction and epithelial to mesenchymal transition. As in other parts of the development graph, the development of a tissue would include much more than this, including morphogenic shaping of cell layers, patterning, selective apoptosis etc, depending on the tissue. Therefore formation terms are made as parts of the morphogenesis terms, and the full morphogenetic process also requires structural organization step to fully generate and organize the structure.

=Structural Organization vs Morphogenesis=

These are not synonymous because the structure has to be initially formed before it can increase in size and be organized. Morphogenesis covers both formation and structural development.

=What is maturation?=

The maturation term was instantiated for cases in which a cell is not changing morphologically (changing shape), but is still developing. The remaining development steps involve synthesis of gene products that will enable the cell or structure to become fully functional.

One example of this is the maturation of the epithelial cells of the intestinal crypts. These are born at the bottom of the crypts as columnar epithelial cells. The process making them conform to this shape is be their morphogenesis. As they mature, they don't change shape, but they move up along the villus due to the death of the cells at the tip and the birth of new cells at the bottom.

While they are moving up, they are synthesizing the gene products that make them functional absorptive cells. This is part of their maturation. Eventually they apoptose. This is also part of their maturation.

Another example would be a neuron that has already fully extended its axons and dendrites (neuron morphogenesis) and is receiving signals about what kind of receptors and neurotransmitters it is going to make. This is maturation because the process doesn't have anything to do with creating the shape of the cell but is required for attainment of full function.

To summarize, the maturation terms capture the processes that are involved in a cell becoming fully functional but that aren't directly related to the changes in shape of the cell.

=Metamorphosis vs Morphogenesis=

The concepts of metamorphosis and morphogenesis are closely related but have some key differences.

[i] x development
[p] x morphogenesis
[i] x metamorphosis

Metamorphosis terms refer to the radical change in shape of a whole organism, for example metamorphosis of the whole tadpole to the whole frog. Morphogenesis terms capture the processes in which the shape or form of a whole organism or part of an organism is gradually formed, for example morphogenesis of a worm, a leaf, or a limb.

* '''x metamorphosis:''' A change of shape or structure of the whole organism from one developmental stage to another, particularly the rapid post embryonic structural transformation from larval to adult form.
* '''x morphogenesis:''' The process in which the anatomical structures of x are generated and organized.

Note that morphogenesis terms always include the name of the mature anatomical part in the term name.

==Imaginal Discs==

The fly imaginal disc terms are a fusion of these two concepts as the process of fly imaginal disc morphogenesis changes the shape of a part of an organism (imaginal disc) very radically. In addition to this, the standard morphogenesis definitions will not work for imaginal disc morphogenesis as the relationship of the initial structures to the mature structures is not one-to-one. One disc can contribute to more than one mature structure, and one structure can be formed from more than one disc. For example, the Drosophila eye-antennal disc gives rise to the eye, antenna, head capsule and maxillary palps. In higher Diptera, primordia contained in different imaginal discs (labial disc, clypeolabral bud) participate in the formation of the proboscis.

Because of this, the research community investigates these processes by looking at the morphogenesis of each disc as a whole, through time, rather than looking at the formation of each individual mature structure. This means that the research results available to be annotated to the GO tend to be couched in terms of disc morphogenesis rather than in terms of morphogenesis of a single anatomical part that happens to be derived from a disc.

The standard morphogenesis terms in GO have the mature anatomical part in the term name and define the process as the steps leading to the final form of that structure. This is not possible in the case of fly imaginal discs and so a slight modification had been made to accommodate the difference in research method, but preserve the standard temporal factors in the description of the process.

Imaginal disc terms receive the name x imaginal disc morphogenesis and the exact synonym x imaginal disc metamorphosis, in which the x refers to the initial anatomical structure. Their definition is very similar to the morphogenesis standard definition but with a key difference:

* '''x morphogenesis:''' The process in which the anatomical structures of x are generated and organized.
* '''x metamorphosis:''' A change of shape or structure of the whole organism from one developmental stage to another, particularly the rapid post embryonic structural transformation from larval to adult form.
* '''x imaginal disc morphogenesis:''' The process in which the anatomical structures derived from the x disc are generated and organized. This includes the transformation of a x imaginal disc from a monolayered epithelium in the larvae of holometabolous insects into the recognizable adult structures a, b, c, d and e. exact synonym: x imaginal disc metamorphosis

The definition still captures the morphogenesis of the mature structure but the immature structure is the one explicitly named in the term name and definition, as in the biological literature. Anyone annotating to these terms should bear in mind that the imaginal disc terms are to be used for annotation of gene products involved in the processes that enable the morphogenesis of the disc (mentioned in the term name) to another anatomical part. This is different from the standard morphogenesis terms in which the term is intended to be used for annotation of gene products involved in morphogenesis bringing about the shape of the part mentioned in the term name. It is important that these differences should be borne in mind while annotating.

In summary, when using these terms, as with all GO terms, please read the definition carefully.

=Differentiation vs Cell development=

Difference between 'cell differentiation' and 'cell development: Cell development should NOT include the steps involved in committing a cell to a specific fate. Differentiation includes the processes involved in commitment. Development is what the cell does once it is committed to a given fate.

To express this our standard structure is like this:

[i] cell differentiation
[p] cell fate commitment
[p] cell development

==When does development start?==

The situation above illustrates a central point in capturing developmental processes in an ontology. The conceptual difficulty here is deciding when the development of x begins and when it ends. For example, the embryogenesis of my mother could be considered to be part of my development, or gastrulation could be considered to be part of kidney development. Although my mother's embryogenesis led to the final state that was me, and gastrulation leads to the final state of a kidney, clearly there has to be a cut-off somewhere.

That cut off is determined by how the class development differs from the class X development. Clearly for the case of me from a biological perspective, the start can be set at the fertilised egg (although that is still argued in legal circles, and ontologists might argue that the individual is not established until the point when it is too late for the egg to divide to produce two individuals). But what about the development of a specific type of cell? It makes sense to set the start of development of a specific type of cell as occurring once the cell has been committed to its fate. Otherwise we may be considering processes that might not necessarily end in the maturation of that cell type. This is how we have expressed the situation in the process ontology.

==Should we represent cell lineage in the process ontology?==

One further related question that we often come up against is whether to try to represent cell lineage in the development node of the process ontology. Lineage relationships are better represented in other ontologies such as in the cell ontology or in an anatomical ontology. The sum of all processes that lead up to something can then be computed based on those relationships. For example, you may want to know about gene products involved in neuron development and you may want to include the development of all the precursors of the neuron. To do this you can use a combination of the cell type ontology (which encodes lineage information) and the development node of the process ontology (which captures information on development). Source: [https://sourceforge.net/p/geneontology/ontology-requests/2794/ SourceForge discussion]

===What is the difference between 'cell differentiation' and 'cell development'?===
Cell development should NOT include the steps involved in committing a cell to a specific fate. Differentiation includes the processes involved in commitment. Development is what the cell does once it is committed to a given fate.

=Cell fate specification, determination and commitment=

The differences between cell fate commitment, cell fate specification and cell fate determination are fairly subtle and so they are explained below.

[i] cell differentiation
[p] cell fate commitment
[p] cell fate specification
[p] cell fate determination

Source: [http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/meeting/minutes/20030125_StCroix.txt?rev=1.1;content-type=text%2Fplain 2003 St. Croix consortium meeting]) + subsequent changes.

* '''cell differentiation:''' The process whereby relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organisms life history.
* '''cell fate commitment:''' The commitment of cells to specific cell fates and their capacity to differentiate into particular kinds of cells. Positional information is established through protein signals that emanate from a localized source within a cell (the initial one-cell zygote) or within a developmental field.
* '''cell fate specification:''' The process involved in the specification of cell identity. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment.
* '''cell fate determination:''' The process involved in cell fate commitment. Once determination has taken place, a cell becomes committed to differentiate down a particular pathway regardless of its environment.

=Cell maturation and differentiation of derivative cell types=

What is the relationship between maturation of a cell type and differentiation of the derivative cell type in the GO process ontology?

To figure this out we have to think about how one cell type arises from another, and then consider how this information is represented in the GO process ontology and in the cell type ontology.

If we consider a cell type A, the differentiation of this cell will include all the steps common to cell differentiation (standard structure and Figure 1). During the differentiation of a cell type A it is possible that some individual cells of the population of A cells will undergo a change of identity to become committed to other cell fates, B and C (Figure 1). This change in identity can occur at any time during the differentiation of a cell of type A. For example in Figure 1 the change of identity is shown as occurring at the end of an instance of cell type A's fate determination step (one A cell giving rise to an one B cell that will then develop). This change in identity is the cell fate commitment of cell type B.

Another instance of cell type A may further mature and be recommitted at another time to give rise to an instance of a cell type C. So, in this case, a cell type A can give rise to both cell type B and cell type C. The lineage information is not reflected in the biological process ontology, but is rather reflected in the cell ontology.

[[Image:Diag-cell-dev.png]]

Figure 1: the steps in the differentiation of the three cell types A, B and C. Cell types B and C are derived from A.

The figure shows that the differentiation of a cell type begins as soon as the process of cell fate specification occurs. In the GO process ontology this would be represented as three separate cell differentiation terms (with appropriate child terms) without any lineage information as follows:

[[Image:Diag-differentiation.png]]

Figure 2: cell differentiation terms and child terms for cell types A, B and C. The background is highlighted in three colours to make it easier to see where the terms for the three different cell types are.

The lineage information would be captured in the cell type ontology as follows ([d]represents the relationship develops_from):

[i] cell by lineage
[i] A cell
[d] B cell
[d] C cell

=A part_of problem for cell differentiation=

There is a potential problem with the use of necessarily is_part in the relationship between the differentiation terms and their parent development terms. If '''cell type X''' cell differentiation occurs as part of the development of two different types of tissue (e.g. '''anatomical structure A''' development and '''anatomical structure B development''') then that would not work with the necessarily is_part kind of part_of relationship that is used in GO. With necessarily is_part, '''X''' cell differentiation doesn't always have to occur during '''B''' development, but '''X''' cell differentiation must only occur as part of '''B''' development.

[i] anatomical structure A development
[p] cell type X cell differentiation
[i] anatomical structure B development
[p] cell type X cell differentiation

'''This structure is incorrect.'''

The solution: A separate term must be made for the differentiation of the cell type in every different organ in which it is found. The standard composition of these terms can be summarized as:

[anatomical structure] + [cell type] + cell differentiation

[i] anatomical structure A development
[p] anatomical structure A cell type X cell differentiation

...

[i] anatomical structure B development
[p] anatomical structure B cell type X cell differentiation

...

[i] cell type X cell differentiation
[i] anatomical structure A cell type X cell differentiation
[i] anatomical structure B cell type X cell differentiation

A practical example:

[i] lung epithelium development
[p] lung epithelial cell differentiation

...

[i] glomerular epithelium development
[p] glomerular epithelial cell differentiation

...

[i] epithelial cell differentiation
[i] heart epithelial cell differentiation
[i] glomerular epithelial cell differentiation

=History of the Development node=

* 2002: Many of the 'development' and 'morphogenesis' terms were written before we had clearly defined the difference between these two concepts and as a consequence both their positions in the ontology and their definions were basically interchangeable. Many of the other standard terms under the development node were also defined using the names of different terms rather than a clear and correct definition.
* 2003: The development interest group developed standard definitions and a standard ontology structure for the terms under the development node.
* 2004: Implementation of the structure began as follows:
** The terms x cell fate commitment, x cell fate specification and x cell fate determination were given their standard definitions.
** x development terms were given their standard definition.
** x morphogenesis terms with definitions that did not include the word 'development' were given their standard definition.
** x cell differentiation terms were given their standard definitions.
** x structural organization generic parent was added for child terms already present.
* 2005: Terms covering the metamorphosis of fly imaginal discs were all converted to morphogenesis terms, with metamorphosis as synonyms. The top metamorphosis terms were retained for use in describing whole body metamorphosis.
* 2005-2006: Morphogenesis standard graph and definitions retrofitted.
* After 2006: Maturation standard graph and definitions retrofitted.

----
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[[Notes_on_specific_terms |Back to: Notes on specific terms]] Pascale
Categories: GO Internal

Membranes and Envelopes

GO wiki (new pages) - Tue, 07/03/2018 - 05:49

Pascale: Created page with "=Terms and structure= GO distinguishes single and double membranes surrounding organelles: an organelle envelope ; GO:0031967 is defined as two lipid bilayers plus the space,..."

=Terms and structure=
GO distinguishes single and double membranes surrounding organelles: an organelle envelope ; GO:0031967 is defined as two lipid bilayers plus the space, or lumen, between them, whereas an organelle membrane ; GO:0031090 is defined as a single bilayer. For double-membrane organelles, the membrane term refers to either of the lipid bilayers, but excludes the intermembrane space. The envelope is part of the organelle and is a organelle envelope ; GO:0031967; the membrane is part of the envelope, and inner membrane and outer membrane terms can be included:

chloroplast
[p] chloroplast envelope
[p] chloroplast membrane
[i] chloroplast inner membrane
[i] chloroplast outer membrane

...

organelle envelope
[i] chloroplast envelope

=History=
Prior to December 2005, nuclear envelope ; GO:0005635 was named 'nuclear membrane', with 'nuclear envelope' as a synonym; this reflected a usage fairly common in the literature. For consistency with other organelle envelope and membrane terms, GO:0005635 is now named 'nuclear envelope', consistent with its definition, and a separate term, nuclear membrane ; GO:0031965, has been added.

=Standard Definitions=

organelle envelope
The double lipid bilayer enclosing the organelle and separating its contents from the rest of the cytoplasm; includes the intermembrane space.
organelle membrane, organelle with a single membrane
The lipid bilayer surrounding a(n) organelle.
organelle membrane, organelle with a double membrane
Either of the lipid bilayers that enclose the organelle and form the organelle envelope.
organelle inner membrane
The inner, i.e. lumen-facing, lipid bilayer of the organelle envelope.
organelle outer membrane
The outer, i.e. cytoplasm-facing, lipid bilayer of the organelle envelope.
organelle membrane lumen
The region between the inner and outer lipid bilayers of the organelle envelope.

=Standard synonyms=
The following synonym can be added to terms as long as the synonym string makes sense and does not have alternative meanings. Note that the term name and synonym can be switched depending on typical usage.

organelle membrane lumen
exact_synonym: organelle intermembrane space




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Back to [[Notes_on_specific_terms]] Pascale
Categories: GO Internal

Metabolic process

GO wiki (new pages) - Tue, 07/03/2018 - 05:41

Pascale:

=Terms and structure=

The process of metabolism includes both biosynthetic and catabolic processes. We also distinguish between metabolism that occurs at the level of a multicellular organism (organismal metabolism) and metabolism that occurs at the level of the cell (cellular metabolism). These subclasses also apply to biosynthesis and catabolism.

Metabolic processes can be described as being organismal when they occur in more than one cell type. An example of this is C4 photosynthesis, a type of carbohydrate biosynthesis achieved with the involvement of two cell types, bundle sheath cells and mesophyll cells. Metabolic processes that are restricted to a single cell or cell type are described as cellular metabolism. The vast majority of metabolic processes are cellular, so unless a corresponding organismal metabolism occurs, we do not add "cellular" to the term name.

For example, during digestion, carbohydrate catabolism occurs first in the mouth, by salivary amylase, and then in the stomach. This process would be described as organismal carbohydrate catabolic process. However, carbohydrate catabolic processes also occurs within a single cell, e.g. glycolysis, so we also need a cellular carbohydrate catabolic process term:

metabolic process
[i] catabolic process
[i] carbohydrate catabolic process
[i] cellular carbohydrate catabolic process
[i] organismal carbohydrate catabolic process
[i] cellular catabolic process
[i] cellular carbohydrate catabolic process
[i] organismal catabolic process
[i] organismal carbohydrate catabolic process

The general structure of metabolic process terms is this:

substance metabolic process
[i] cellular substance metabolic process
[i] cellular substance biosynthetic process
[i] cellular substance catabolic process
[i] organismal substance metabolic process
[i] organismal substance biosynthetic process
[i] organismal substance catabolic process
[i] substance biosynthetic process
[i] cellular substance biosynthetic process
[i] organismal substance biosynthetic process
[i] substance catabolic process
[i] cellular substance catabolic process
[i] organismal substance catabolic process

However, remember that most types of metabolism are children of cellular metabolic process (or cellular biosynthetic process, cellular catabolic process), and do not have the modifier 'cellular'.

For example, where substance A and substance B metabolic process are cellular processes:

metabolic process
[i] cellular metabolic process
[i] substance A metabolic process
[i] substance A biosynthetic process
[i] substance A catabolic process
[i] substance B metabolic process
[i] substance B biosynthetic process
[i] substance B catabolic process
[i] cellular biosynthetic process
[i] substance A biosynthetic process
[i] substance B biosynthetic process
[i] cellular catabolic process
[i] substance A catabolic process
[i] substance B catabolic process

=Standard Definitions=

* '''substance metabolic process''': The chemical reactions and pathways involving substance, [description of substance].
* '''substance biosynthetic process''': The chemical reactions and pathways resulting in the formation of substance, [description of substance].
* '''substance catabolic process''': The chemical reactions and pathways resulting in the breakdown of substance, [description of substance].
* '''substance fermentation''': The enzymatic conversion of substance to simpler components, resulting in energy in the form of adenosine triphosphate (ATP).

=Other standard metabolic processes=
==Salvage and de novo biosynthesis==

Biosynthesis can be further split up into those processes that create a substance from scratch and those that use derivatives of the substance. The ontology structure is as follows:

metabolic process
[i] biosynthetic process
[i] 'de novo' biosynthetic process
[i] salvage
[i] catabolic process

*'''substance salvage''': Any process that produces substance from derivatives of it, without de novo synthesis.
*'''substance 'de novo' biosynthetic process''': The chemical reactions and pathways resulting in the formation of substance from simpler precursors.

=Standard Synonyms=
The following synonyms should be added to metabolic process terms unless the synonym does not make sense or it has a specialised meaning that conflicts with the intended usage.

substance metabolic process
exact: substance metabolism
substance biosynthetic process
exact: substance anabolism
exact: substance biosynthesis
exact: substance formation
exact: substance synthesis
substance catabolic process
exact: substance breakdown
exact: substance catabolism
exact: substance degradation
substance salvage
exact: substance salvage pathway
substance 'de novo' biosynthetic process
exact: 'de novo' substance anabolism
exact: 'de novo' substance biosynthesis
exact: 'de novo' substance formation
exact: 'de novo' substance synthesis

=Qualifiers=
The following qualifiers can be used with metabolic process, biosynthetic process and catabolic process terms. The examples given use the metabolic process term but the standard definitions for biosynthetic process and catabolic process can be substituted into the definition in its place.

cellular substance metabolic process
The chemical reactions and pathways involving substance, as carried out by individual cells.
organismal substance metabolic process
The chemical reactions and pathways involving substance, occurring at the tissue, organ, or organismal level of a multicellular organism.
aerobic substance metabolic process
The chemical reactions and pathways involving substance in the presence of oxygen.
anaerobic substance metabolic process
The chemical reactions and pathways involving substance in the absence of oxygen.
X-dependent substance metabolic process
The chemical reactions and pathways involving substance, requiring the presence of X.
X-independent substance metabolic process
The chemical reactions and pathways involving substance, independent of X.

More complex metabolic process terms to represent specific processes can be constructed by adding one or more of the following suffixes to a term name and altering the definition as appropriate.

substance A biosynthetic process from substance B
The chemical reactions and pathways resulting in the formation of substance A from other compounds, including substance B.
substance A catabolic process to substance B
The chemical reactions and pathways resulting in the breakdown of substance A into other compounds, including substance B. Can also be used with fermentation terms.
substance A catabolic process via substance C
The chemical reactions and pathways resulting in the breakdown of substance A into other compounds, via the intermediate substance C. Can also be used with biosynthetic process and fermentation terms.
substance A catabolic process, using enzyme
The chemical reactions and pathways resulting in the breakdown of substance A, catalyzed by enzyme. Can also be used with biosynthetic process and fermentation terms.
substance A catabolic process, X pathway
The chemical reactions and pathways resulting in the breakdown of substance A, by the X pathway. Can also be used with biosynthetic process and fermentation terms.
substance A catabolic process, X cycle
The chemical reactions and pathways resulting in the breakdown of substance A in the X cycle. Can also be used with biosynthetic process and fermentation terms.
substance A catabolic process, by biochemical process
The chemical reactions and pathways resulting in the breakdown of substance A, by biochemical process. Can also be used with biosynthetic process and fermentation terms.

For example:

L-lysine catabolic process to glutarate, by acetylation
The chemical reactions and pathways resulting in the breakdown of L-lysine into other compounds, including glutarate, by acetylation.
glucose biosynthetic process from tryptophan via maltose and cystathione, using sucrose invertase
The chemical reactions and pathways resulting in the formation of glucose from other compounds, including tryptophan, via the intermediates maltose and cystathione, catalyzed by sucrose invertase.

=Different pathways or processes leading to the same product=
Where there are several biosynthetic pathways leading to the same product, we list each of them as a subclass of a general pathway.

For example, we have:

glucose catabolic process ; GO:0006007
[i] glycolysis ; GO:0006096
[i] pentose-phosphate shunt ; GO:0006098

It is straightforward to name well-known pathways (e.g. glycolysis and the pentose-phosphate pathway are two ways to accomplish glucose catabolic process), but harder for nameless minor pathways. Minor pathways should be named by referring to start and end products, and intermediates if further distinguishing is required.

For example:

L-arabinose catabolism ; GO:0019572
[i] L-arabinose catabolism to 2-oxoglutarate ; GO:0019570
[i] L-arabinose catabolism to xylulose 5-phosphate ; GO:0019569


[[Category:GO Editors]][[Category:Ontology]]
Back to [[Notes_on_specific_terms]] Pascale
Categories: GO Internal

Transmembrane Proteins

GO wiki (new pages) - Mon, 07/02/2018 - 08:28

Vanaukenk: /* Legacy Transmembrane Protein Annotations = */

= Annotating Transmembrane Proteins =
*Subcellular localization of transmembrane proteins is often determined by methods that do not specifically address the precise topology of the protein.
*For example, immunofluorescence experiments using fusion proteins or antibodies, as well as experiments that label and detect cell surface proteins, may be used to confirm localization of a transmembrane protein to a plasma, or organellar, membrane.
*For GO Cellular Component curation, it is acceptable to annotate a protein containing a predicted transmembrane domain to an appropriate child of GO:0016021, 'integral to membrane' using such experiments as supporting evidence if the following conditions are met:
**Sequence analysis of the protein being annotated support the existence of one or more transmembrane domains
**The experiments clearly demonstrate localization to the plasma membrane or the membrane of a subcellular organelle
**The active protein is believed to be the transmembrane-localized protein

= Legacy Transmembrane Protein Annotations =



Back to: [[Annotation]]

[[Category: Annotation]] Vanaukenk
Categories: GO Internal

Ontology meeting 2018-07-02

GO wiki (new pages) - Fri, 06/29/2018 - 05:56

David: /* Obsoletion plugin for Protege */

= Conference Line =

*Zoom: https://stanford.zoom.us/j/828418143

= Agenda =

== Editors Discussion ==

===Project Update===
====ECM Project--- https://github.com/geneontology/go-ontology/projects/9====

=== Regenerate Imports File ===
Erich, David, Kimberly and Pascale loaded Docker and tried to regenerate the cell ontology import but were unsuccessful.

Erich think he has solved the issue. We will try again this week.

=== Obsoletion plugin for Protege ===
Please add you Protege versions and the plugin you have here.

Barbara- Protege 5.2.0 <br>
David- Protege 5.1.0, OBO annotation plugin 0.4.0<br>
Harold- Protege 5.1.0, OBO annotation plugin 0.4.0<br>
Karen- Protege 5.1.0 <br>
Kimberly- Protege 5.1.0, I have something called OBO annotation editors 0.3.0 - is that the plugin? <br>

=== Ontology Documentation ===
Pascale, David and Kimberly have been working on standardizing the ontology documentation to make it align with the documentation work that Kimberly and Pascal have been doing for other areas of GO. Specifically, we have moved the official documentation to the wiki and have arranged the wiki in a way that is similar to the annotation section. We are now going through the documentation to check it for accuracy and to be sure it is up to date.

Last week Pascale and David worked on the definitions section.


===Ontology Developers' workshop possibility===
* Push to November

==GH project link==
https://github.com/geneontology/go-ontology/projects/1

= Minutes =
*On call:




[[Category: Ontology]]
[[Category: Meetings]] David
Categories: GO Internal

Manager Call 2018-07-19

GO wiki (new pages) - Wed, 06/27/2018 - 10:21

Pascale: Created page with "Category:GO Managers Meetings (These topics were moved from the June 20th call) ==From PI call== Managers should help define the tasks of the helpdesk group Proposal:..."

[[Category:GO Managers Meetings]]

(These topics were moved from the June 20th call)
==From PI call==
Managers should help define the tasks of the helpdesk group

Proposal: (Pascale)
* monitor helpdesk repo
* monitor Biostars for GO-related questions


Managers should help define the tasks of the outreach group
* help new groups make annotations submissions

== Topics not discussed at last meeting ==

* create a simple challenge form? (see noctua new user form)
* licensing and "remix" for upstream sources (e.g. Reactome)
* licensing sign-over or statement (annotation input)
* zenodo and user metadata; proposal: "active" users and cull users.yaml (possibly a small sub-group from there, about half an hour)
* Laurent-Philippe: collect information / links / contacts about the GO user communities (e.g. R/bioconductor and ?)
* (Pascale) Rules, especially taxon checks: can we have this for the July release? https://github.com/geneontology/go-annotation/issues/1928


==Minutes== Pascale
Categories: GO Internal

Noctua Technical Call 2018-06-27

GO wiki (new pages) - Tue, 06/26/2018 - 14:19

Vanaukenk: /* Meeting Time Change */

= Meeting URL =
https://stanford.zoom.us/j/679970729
== Meeting Time Change ==
*To give the West Coast a break from the 8am GO meetings, we are thinking of changing the time of this meeting.
*How about 11am/2pm on Wednesdays?

= Agenda =

== Internals ==
*From 5/23 meeting:
* refactoring
* stack alignment
** common widgets/UI
* paying down debt
* functional parity
** live updates
** login and groups across clients and workbenches

== Annotation ==
* If there is plan to just have an update minerva API, preferably batch update just like currently adding multiple entities at the same time. Altering the individual class expression on that low level is very error-prone. For example I just found out, changing the term and evidence is 2 separate processes. (Tremayne)
*Editing ('conventional' and GO-CAM)
**Tremayne working on an editing interface
**Curators can search for gene/gene product ID, GO term, Reference
**Matches will then be presented in a form view for editing with links to a model, if applicable
*Model cloning

== Error checks ==
*The Form to use Reasoner or centralised checker through API to check for errors. I think Noctua Form error checking was for 1.0 release. It depends heavily on golr and different way than Reasoner. I think we should have one definition of an model activity (algorithm wise). Bcz there will be cases where the graph says there is an error and Form doesn't catch it then. (Tremayne)
*Incorporating annotation rules into Noctua
**Some annotation errors are flagged in the form editor
**Others may need to get checked during the release pipeline
***Curators may wish use lines from GPAD file in order to retrieve the correct model id if they want to edit starting from a model URL

== Landing Page ==
*I have a particularly blocking issue with NEO and URIs that prevents me to correctly display the name of genes when browsing the models. (Laurent-Philippe)
*Model searching (production)
*Model titles - need guidelines
**This issue is still outstanding, but is maybe not as big an issue now that we can search over more terms, additional metadata, etc.
*Different landing pages for public vs curators?

== Model Seeding ==
*From GAFs
*From Reactome

== Relations ==
*Reconcile CC annotation relations with CC ontology relations
*Use of has_input vs has_participant for binding annotations
*David, Pascale, and Kimberly reviewing all relations used in GO and their documentation

== Templates ==
*Create and use templates for curation

== GPAD Outputs ==
*Protein complexes
**This will need to be one of the high priority tasks for the working group (see below)
**Emergent functions will need to be handled differently from functions where one of the subunits actually enables the activity of the complex
*Annotation extension relations white list
**How do we want to handle this?
**Do groups want to see all possible extensions and then filter at their respective MODs?
**If we do that, are there any possibilities for inconsistent display between MODs and AmiGO?

== Text Mining ==
*TPC integration into form
**Will draw up requirements for this and hope to make progress before and/or during the late August hackathon at USC

[[Category: Annotation Working Group]] Vanaukenk
Categories: GO Internal

GO-CAM Working Group Call 2018-06-26

GO wiki (new pages) - Mon, 06/25/2018 - 12:04

Vanaukenk: /* Noctua */

= Meeting URL =
https://stanford.zoom.us/j/976175422

=Agenda=
== Logistics ==
*User accounts
**Follow-up from last week: Sandy L
**https://github.com/geneontology/noctua/issues/563
***Closed - all okay
*Groups
**https://github.com/geneontology/noctua-models/issues/96
***Should this be discussed on Wednesday's technical call?

== Noctua ==
*[http://geneontology.org/gocam Landing Page (under development)]
**Browsing GO-CAMs
**User and Group Pages
**Curators should look around the landing page, provide feedback

== Documentation ==
*[http://wiki.geneontology.org/index.php/Noctua Noctua tool]
*[http://wiki.geneontology.org/index.php/Annotation_Relations Annotation relations]

== Proposal for this group ==
*Focus on specific, commonly used curation modules
**For example, transcription, signaling pathways, metabolic pathways
*Groups will annotate papers of their own choosing
*We will discuss representation of the data in GO-CAMs, and any questions or issues that arise
**Choosing the appropriate relation
**Assigning evidence
*Give feedback to tool developers, ontology editors based on our discussions
**Github trackers
***[https://github.com/geneontology/noctua noctua]
***[https://github.com/geneontology/simple-annoton-editor simple annoton editor]
***[https://github.com/geneontology/go-ontology go-ontology]
*Develop additional documentation

=Minutes=
*On call: Dustin, Giulia, Jim, Kimberly, Laurent-Philippe, Penelope, Rob, Sabrina, Sandy L, Stacia, Suzi A, Suzi L

== Noctua ==
*Current landing page provides links to form and graph editors
*Landing page under development provides additional model search functionality, links to curator reports, information about GO terms in models
**Could be used to help identify related curation and experts who can review models on specific areas of biology

*Sabrina asked about what happens to group affiliation on older models if a curator is no longer with that group?
**Check with Seth, but the group affiliation at the time of model curation will likely remain unless the curator specifically requests that it be changed - use the noctua-models tracker to do this
**Removing an affiliation from a users.yaml entry should not affect affiliations in existing models

== QA/QC ==
*Noctua does not yet have taxon restrictions for annotation
**Will be added in the future
*gp2term relations for legacy annotations
**High priority for this summer is to address existing BP annotations and develop as many rules-based approaches for applying new relations as possible
**Whatever annotations are left will need to be manually reviewed by curators

== Curation Projects for this Group ==
*Will try creating models for papers that describe transcriptional regulation
*A caveat to this is that right now the MF branch for transcription factors is still under review, so we may have to make some changes to annotations in the future
**However, it would still be good to work out the relations between the MFs and the BPs wrt transcription and upstream and downstream activities and processes
*[https://docs.google.com/document/d/1icc1pb3mRFb4kK_ELVY1rjqxEjXNehrQzelWTqM-ZD4/edit# Google doc for entering papers and curation questions]





















[[Category: Annotation Working Group]] Vanaukenk
Categories: GO Internal

2018 Montreal GOC Meeting Logistics

GO wiki (new pages) - Mon, 06/25/2018 - 08:32

Pascale:


=Start and end of meeting=


=Registration fee=


=Meeting site=


=Call-in information=


=Travel=



=Accommodations=




=Food=


=Bicycling and walking / running=


=Attendees=
Please add your name to the table if you intend to attend the meeting, and the dinner, so we can get a headcount estimate.
{| {{Prettytable}} class='sortable'
|-
! Name
! Organization
! Attend the GOC dinner?
|-
| Pascale Gaudet
| SIB/GO Central
| Yes
|-
|}

=Remote attendees=
If you plan to attend remotely, please sign up here and indicate the sessions you are likely to attend:
{| {{Prettytable}} class='sortable'
|-
! Name
! Organization
|-
|}

[[Category: GO Consortium Meetings]] Pascale
Categories: GO Internal

2018 Montreal GOC Meeting Agenda

GO wiki (new pages) - Mon, 06/25/2018 - 08:24

Pascale: /* New topics */

= AGENDA=




== Suggestions for topics Fall 2018==
===Carried over from May 2018===
*'Response to' workshop (similar to the signaling WS)
* Documentation of rules: Which annotation validation rules are currently implemented? https://github.com/geneontology/go-annotation/issues/1928
* Use cases: Should we add this to the agenda? What would be a productive way of discussing this topic? https://docs.google.com/document/d/104m4jUNjPH9pCpskg8E29Zm2pLHhPFmKyIFLa9l_EOQ/edit


===New topics===
* Which organisms other than cerevisiae and pombe have looked at all protein coding genes for the availability/possibility of GO annotation? If anyone is interested, there is a very quick/easy way to establish the difference between: (1) "not in the GO database (not found); (2) "unknown" (ND), and (3) "unannotated" (no ND, and no annotation in Aspect of interest) for your organisms proteins using the complete known protein ID set for your organism and the GO term mapper tool https://go.princeton.edu/cgi-bin/GOTermMapper
(GOTermMapper provides these numbers as part of the output so that the slim set results can be interpreted correctly).
(Val)

[[Category: GO Consortium Meetings]] Pascale
Categories: GO Internal

Ontology meeting 2018-06-25

GO wiki (new pages) - Mon, 06/25/2018 - 06:01

David: Created page with "= Conference Line = *Zoom: https://stanford.zoom.us/j/828418143 = Agenda = == Editors Discussion == ===Project Update=== Rhea-Reactome_GO alignment--- https://github.com/g..."

= Conference Line =

*Zoom: https://stanford.zoom.us/j/828418143

= Agenda =

== Editors Discussion ==

===Project Update===
Rhea-Reactome_GO alignment--- https://github.com/geneontology/go-ontology/projects/10


=== Regenerate Imports File ===
We continue to have issues with imported files. Although we can modify the import files, this isn't really a solution.

=== Obsoletion plugin for Protege ===
Please add you Protege versions and the plugin you have here.


=== Ontology Documentation ===
Pascale, David and Kimberly have been working on standardizing the ontology documentation to make it align with the documentation work that Kimberly and Pascal have been doing for other areas of GO. Specifically, we have moved the official documentation to the wiki and have arranged the wiki in a way that is similar to the annotation section. We are now going through the documentation to check it for accuracy and to be sure it is up to date.


===Ontology Developers' workshop possibility- Geneva in September?===
* David, Pascale and Kimberly will discuss possible dates and make a doodle poll.


==GH project link==
https://github.com/geneontology/go-ontology/projects/1

= Minutes =
*On call:





[[Category: Ontology]]
[[Category: Meetings]] David
Categories: GO Internal