aurelian 0.3.2__py3-none-any.whl

aurelian/agents/gocam/documents/md/Protein_sequestering_activity.md

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+Guidelines for annotating molecular sequestering
+activity
+A sequestering activity is defined as the binding to a specific molecule to prevent it from
+interacting with other partners or to inhibit its localization to the area of the cell or complex
+where the target is active.
+
+Pathway Editor
+The activity unit for a molecular sequestering activity is:
+● MF: molecular sequestering activity (GO:0140313). The most commonly used
+child is protein sequestering activity (GO:0140311).
+●
+
+Context:
+○ The relation between the protein that act to sequester and its target is 'has
+input'
+○ BP: 'part of' negative regulation of the BP in which the target protein
+participates .
+○ CC: the location where the activity occurs.
+○ The causal relation between the sequestering activity and the activity of the
+protein it inhibits is 'directly negatively regulates' because there is a direct
+interaction between the two proteins.
+
+Example 1: Sequestering activity of CAV1 negatively regulates TLR4 signaling
+
+Example 2: Trans-negative regulation of Sars-CoV-2 viral entry into host cell
+by LRRC15.
+
+Form Editor
+The activity unit for sequestering activity is:
+●
+●
+
+MF: molecular sequestering activity (GO:0140313) or a child
+Context:
+○ The relation between the protein that act to sequester and its target receptor
+is 'has input'
+○ BP: negative regulation of the BP in which the regulated protein participates
+○ CC: the location where the activity occurs.
+
+Example 1: Sequestering activity of CAV1 negatively regulates TLR4 signaling
+
+Differences between GO-CAM and standard
+annotation of a sequestering activity
+In standard annotation (captured with the Noctua Form or Protein2GO), relations between
+molecular functions are not captured, so there is no relation between the sequestering
+activity and the activity of the protein being sequestered.
+
+Review information
+Review date: 2023-07-25
+Reviewed by: Cristina Casals, Pascale Gaudet, Patrick Masson
+
+

aurelian/agents/gocam/documents/md/Signaling_receptor_activity_annotation_guidelines.md

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+Guidelines for annotating signaling receptor
+activity
+Receptor activation by a ligand is represented differently in GO-CAM depending on whether
+the ligand is (i) a protein (i. e., encoded by a gene) or (ii) a small molecule.
+
+Pathway Editor
+Protein ligand-activated signaling receptor
+Ligand
+The activity unit for a ligand of a signaling receptor is:
+●
+
+MF: a ligand 'enables' receptor ligand activity (GO:0048018) or a child
+
+●
+
+Context:
+o
+o
+o
+
+The relation between a ligand and its target receptor is 'has input'
+BP 'part of' the process in which the ligand participates, usually a child of
+signal transduction (GO:0007165)
+CC:
+▪
+
+extracellular ligands: 'occurs in' extracellular space (GO:0005615)
+
+▪
+
+membrane-bound ligands: 'occurs in' plasma membrane
+(GO:0005886)
+
+o
+
+The causal relation between the ligand activity and the receptor activity is
+'directly positively regulates'.
+
+Signaling receptor
+The activity unit for a signaling receptor is:
+●
+
+MF: 'enables' signaling receptor activity (GO:0038023) or a child.
+
+●
+
+Context:
+o
+o
+
+The input (target) of the receptor is the effector protein it regulates, for
+example a molecular adaptor, captured with the 'has input' relation.
+Note that the input (target) of the receptor is NOT its ligand
+
+●
+
+BP 'part of' the same BP/signal transduction pathway as the ligand
+
+●
+
+CC: transmembrane receptors: 'occurs in' plasma membrane (GO:0005886)
+
+o
+
+The causal relation between the MF of the receptor and the MF of its target
+is 'directly positively regulates'.
+
+Example: Insulin signaling model
+
+Small molecule-activated signaling receptor activity
+●
+
+Since small molecules are not annotated in GO, a small molecule ligand does not
+have a molecular function. Instead, the ligand and the receptor activity are linked
+by the causal relation 'is small molecule activator'.
+
+●
+
+The receptor's function, input, and contextual relations are the same as for protein
+ligand-activated receptors.
+
+●
+
+Note that it is also possible to annotate an inhibitory ligand using the relation 'is small
+molecule inhibitor'.
+
+●
+
+BP and CC annotations are the same as for protein ligand-activated receptor activity.
+
+Example: Activation of a GPCR by succinate
+
+Special cases
+Receptor with coreceptor
+This is common in immune receptors. The typical sequence of events is that the ligand binds
+the signaling receptor, which signals to the co-receptor to activate its downstream effector
+(such as a protein kinase).
+
+Example: IL2 signaling pathway (Human)
+In this case, the receptor is activated by an information biomacromolecule (i.e. a protein).
+Interleukin-2 (IL2), a cytokine, activates its receptor, interleukin-2 receptor A (IL2RA).
+IL2RA directly positively regulates (activates) IL2RB, which phosphorylates and positively
+regulates JAK1.
+The activity unit for a signaling coreceptor is:
+●
+
+MF: coreceptor activity (GO:0015026)
+
+●
+
+Context:
+o
+o
+
+●
+
+The relation between the receptor and its input (target) is the signaling
+coreceptor it regulates, captured with the 'has input' relation
+Note that the input (target) of the coreceptor is NOT the ligand
+
+BP 'part of' the BP in which the signaling receptor is involved, usually a child of signal
+transduction (GO:0007165)
+
+●
+
+CC: transmembrane receptors: 'occurs in' plasma membrane (GO:0005886)
+o
+
+The causal relation between the MF of the receptor and the MF of its
+coreceptor is 'directly positively regulates'.
+
+Note:
+●
+
+cytokine activity is_a receptor ligand activity
+
+●
+
+interleukin-2 receptor activity is_a signaling receptor activity
+
+Form Editor
+Protein ligand-activated signaling receptor
+Ligand activity
+The activity unit for a ligand of a signaling receptor is:
+●
+
+MF: a ligand 'enables' receptor ligand activity (GO:0048018) or a child
+
+●
+
+Context:
+o
+o
+o
+
+The relation between a ligand and its target receptor is 'has input'
+BP 'part of' the BP in which this ligand is involved (usually a child of signal
+transduction (GO:0007165))
+CC:
+▪
+
+extracellular ligands: 'occurs in' extracellular space (GO:0005615)
+
+▪
+
+membrane-bound ligands: 'occurs in' plasma membrane
+(GO:0005886)
+
+●
+
+The causal relation between the ligand activity and the receptor activity is
+'directly positively regulates'.
+
+Example: Insulin signaling model
+
+Signaling receptor activity
+The activity unit for a signaling receptor is:
+
+●
+
+MF: The receptor 'enables' signaling receptor activity (GO:0038023) or a child.
+
+●
+
+Context:
+o
+o
+
+●
+
+The input (target) of the receptor is the effector protein it regulates, for
+example a molecular adaptor, captured with the 'has input' relation
+Note that the input (target) of the receptor is NOT its ligand
+
+BP in which the signaling receptor is involved, usually a child of signal transduction
+(GO:0007165)
+
+●
+
+CC: 'occurs in' a child of cellular anatomical entity (GO:0110165). For
+transmembrane receptors, annotate to plasma membrane (GO:0005886)
+
+Example: Insulin signaling model
+
+o
+
+The causal relation between the MF of the receptor and the MF of its target
+is 'directly positively regulates'.
+
+Small molecule-activated signaling receptor activity
+●
+
+In the Form, small molecules are not captured, so the MF for the receptor. Therefore,
+the MF is 'enables' signaling receptor activity (GO:0038023) or a child.
+
+●
+
+BP and CC annotations are the same as for protein ligand-activated receptor activity.
+
+Receptor with coreceptor
+Example: IL2 signaling pathway (Human)
+In this case, the receptor, interleukin-2 receptor A (IL2RA), is activated by a protein ligand,
+interleukin-2 (IL2). IL2RA directly positively regulates (activates) the coreceptor IL2RB,
+which phosphorylates and positively regulates JAK1.
+
+The activity unit for a signaling coreceptor is:
+●
+
+MF: The coreceptor 'enables' coreceptor activity (GO:0015026) or a child.
+
+●
+
+Context:
+o
+o
+
+●
+
+The input (target) of the coreceptor is the signaling receptor it regulates,
+captured with the 'has input' relation
+Note that the input (target) of the coreceptor is NOT the ligand
+
+BP 'part of' the BP in which the signaling receptor is involved, usually a child of signal
+transduction (GO:0007165)
+
+●
+
+CC: transmembrane receptors: 'occurs in' plasma membrane (GO:0005886)
+
+Note:
+●
+
+cytokine activity is_a receptor ligand activity
+
+●
+
+interleukin-2 receptor activity is_a signaling receptor activity
+
+Differences between GO-CAM and standard annotation of a
+signaling receptor and its ligand
+In standard annotation (captured with the Noctua Form or Protein2GO), relations between
+molecular functions are not captured, so there is no relation between the ligand activity and
+the signaling receptor activity, nor is there a relation between the signaling receptor activity
+and the activity of its target. Likewise for receptor activity and coreceptor activity, there is no
+relation between these activities captured in standard annotations.
+
+Review information
+Review date: 2023-07-20
+Reviewed by: Cristina Casals, Pascale Gaudet, Patrick Masson
+
+

aurelian/agents/gocam/documents/md/Transcription_coregulator_activity.md

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+Transcription coregulator activity
+The activity unit for a transcription coregulator is:
+o
+
+o
+
+MF: a child of transcription coregulator activity (GO:0003712):
+▪
+
+transcription coactivator activity (GO:0003713)
+
+▪
+
+transcription corepressor activity (GO:0003714)
+
+Context:
+▪
+
+has input: the transcription factor regulated, when known.
+
+▪
+
+BP in which this transcriptional event is involved
+
+▪
+
+CC: this activity occurs in the nucleus.
+
+●
+
+The causal relation between the transcription coregulator activity and the transcription
+factor activity unit is ‘directly positively regulates’ or 'directly negatively regulates.
+
+●
+
+If the causal relation between the coregulator and the target gene regulated needs to be
+captured, the causal relation is: ‘indirectly positively regulates’ or 'indirectly negatively
+regulates’, since there are many steps between the regulation of transcription and the
+activity of the target protein.
+
+Example: GO:0003714 transcription corepressor activity
+
+Example: GO:0003713 transcription coactivator activity
+
+Example: GO:0003712 transcription coregulator activity (BMAL1 binds
+specifically DNA)
+
+Example: Coregulator of an unknown transcription factor
+
+Review information
+To be reviewed date:
+Created by: Cristina Casals
+
+

aurelian/agents/gocam/documents/md/Transporter_activity_annotation_annotation_guidelines.md

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+Guidelines for annotating transporter activity
+Pathway Editor
+The activity unit for a transmembrane transporter is:
+● MF: 'enables' a child of transmembrane transporter activity GO:0022857
+● Context:
+○ The movement of the small molecule substrate is represented by:
+■ small molecule (ChEBI) + ‘input of’ + the start location of the small
+molecule, captured with the relation 'located in'
+■ the transporter activity + ‘has output’ the small molecule (ChEBI) + the
+end location of the small molecule, captured with the relation 'located in'
+○ BP 'part of' the BP in which this transporter activity participates
+○ CC 'occurs in' a child of membrane (GO:0016020), e. g.: lysosomal membrane
+(GO:0005765).
+
+Example: SLC17A9 transports ATP to the lysosomal lumen
+
+Form Editor
+The activity unit for a transmembrane transporter is:
+● MF: a child of transmembrane transporter activity GO:0022857
+● Context: The movement of the small molecule substrate is represented by:
+○ 'has input’ the small molecule (ChEBI)
+○ BP 'part of' the BP in which this transporter activity participates
+○ CC 'occurs in' a child of membrane (GO:0016020), e. g.: lysosomal membrane
+(GO:0005765)
+
+Example: SLC17A9 transports ATP to the lysosomal lumen
+
+Differences between GO-CAM and standard
+annotation of a transmembrane transporter activity
+In standard annotation (captured with the Noctua Form or Protein2GO), the localization of the
+molecule is not captured; neither is the output of the transporter, since that output relates to the
+localization of the molecule transported.
+
+Review information
+Review date: 2023-07-20
+Reviewed by:Cristina Casals, Pascale Gaudet, Patrick Masson
+
+

aurelian/agents/gocam/documents/md/WIP_-_Regulation_and_Regulatory_Processes_in_GO-CAM.md

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+Guidelines for annotating regulation and regulatory
+processes in GO-CAM
+Molecular functions, and the biological processes of which they are a part, are often subject to
+some form of regulation, typically in response to changing environmental conditions or stimuli.
+In GO, regulation has a very specific meaning: for one molecular function to regulate another,
+the mechanism must be known, it must occur under specific conditions (i.e. not constant),
+and may be direct (contiguous activities) or indirect (non-contiguous, with intervening
+activities). Regulatory activities may also have a positive or negative effect on the
+downstream activity.
+Examples of regulatory molecular functions include, but are certainly not limited to, protein
+kinase activity, GTPase activator (GAP) activity, and transcription regulator activities.
+Modeling regulation is an important aspect of GO-CAM curation but can differ according to how
+the regulatory activities function in the broader context of the biological process.
+Examples of distinct ways to capture regulation in GO-CAMs are discussed below.
+
+Metabolic pathways and feedback regulatory mechanisms
+Feedback mechanisms in which a product, or output, of one activity in a process inhibits another
+activity in a process (i.e. negative feedback loop) is an important way to regulate metabolic
+processes.
+Feedback loops represent a type of process regulation that is ‘self-contained’, i.e. the regulatory
+activity is not typically part of another, larger regulatory process.
+In these cases, curators include the regulatory activity in the metabolic model and capture the
+output molecules that stimulate the regulation and the causal relation between the regulatory
+and regulated activities.
+An example of this type of regulation is found in the GDP-mannose biosynthetic process
+(GO:0009298), in which the terminal output generated by GMPPB, GDP-alpha-D-mannose,
+binds to, and stimulates the inhibitory activity of, GMPPA on GMPPB.
+Figure 1 shows a cartoon schematic of how GMPPA inhibits GMPPB, while Figure 2 shows how
+this regulation is modeled in GO-CAM as part of the larger metabolic process. for D.
+melanogaster model for GDP-mannose biosynthetic process from glucose (Dmel).
+
+In this model, the output, GDP-alpha-D-mannose, of the terminal activity in the pathway,
+mannose-1-phosphate guanylyltransferase (GTP) activity enabled by Gmppb, is a small
+molecule activator of the enzyme inhibitor activity enabled by Gmppa. When bound to GDPalpha-D-mannose (2-), Gmppa undergoes a conformational change that then inhibits catalytic
+activity of Gmppb.
+
+https://www.nature.com/articles/s41594-021-00591-9
+
+