aurelian 0.3.2__py3-none-any.whl

aurelian/agents/gocam/documents/Transcription_coregulator_activity.md

@@ -0,0 +1,36 @@
+## **Transcription coregulator activity**
+
+The activity unit for a transcription coregulator is:
+
+* **MF:** a child of transcription coregulator activity ([GO:0003712](https://www.ebi.ac.uk/QuickGO/term/GO%3A0003712)):
+  + transcription coactivator activity ([GO:0003713](https://www.ebi.ac.uk/QuickGO/term/GO%3A0003713))
+  + transcription corepressor activity ([GO:0003714](https://www.ebi.ac.uk/QuickGO/term/GO%3A0003714))
+* **Context:**
+  + has input:the transcription factor regulated, when known.
+  + **BP** in which this transcriptional event is involved
+  + **CC:** this activity occurs in the [nucleus](https://www.ebi.ac.uk/QuickGO/term/GO%3A0005634).
+* 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**](http://noctua.geneontology.org/workbench/noctua-visual-pathway-editor/?model_id=gomodel%3A62900b6400001630)
+
+![](data:image/png;base64...)
+
+### Example: [**GO:0003713 transcription coactivator activity**](http://noctua.geneontology.org/workbench/noctua-visual-pathway-editor/?model_id=gomodel%3A63894f2500001048)
+
+![](data:image/png;base64...)
+
+### Example: [**GO:0003712 transcription coregulator activity**](http://noctua.geneontology.org/workbench/noctua-visual-pathway-editor/?model_id=gomodel%3A648d0dc100000022) (BMAL1 binds specifically DNA)
+
+![](data:image/png;base64...)
+
+### Example: [**Coregulator of an unknown transcription factor**](http://noctua.geneontology.org/workbench/noctua-visual-pathway-editor/?model_id=gomodel%3A62900b6400001630)
+
+![](data:image/png;base64...)
+
+# Review information
+
+To be reviewed date:
+
+Created by: Cristina Casals

aurelian/agents/gocam/documents/Transporter_activity_annotation_annotation_guidelines.md

@@ -0,0 +1,43 @@
+# 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](https://www.ebi.ac.uk/QuickGO/term/GO%3A0022857)
+* **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](https://www.ebi.ac.uk/QuickGO/term/GO%3A0016020)), e. g.: lysosomal membrane ([GO:0005765](https://www.ebi.ac.uk/QuickGO/term/GO%3A0005765)).
+
+**Example:** [**SLC17A9 transports ATP to the lysosomal lumen**](http://noctua.geneontology.org/workbench/noctua-visual-pathway-editor/?model_id=gomodel%3A63f809ec00001779)
+
+![](data:image/png;base64...)
+
+##
+
+## Form Editor
+
+The activity unit for a transmembrane transporter is:
+
+* **MF**: a child of transmembrane transporter activity [GO:0022857](https://www.ebi.ac.uk/QuickGO/term/GO%3A0022857)
+* **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](https://www.ebi.ac.uk/QuickGO/term/GO%3A0016020)), e. g.: lysosomal membrane ([GO:0005765](https://www.ebi.ac.uk/QuickGO/term/GO%3A0005765))
+
+**Example:** [**SLC17A9 transports ATP to the lysosomal lumen**](http://noctua.geneontology.org/workbench/noctua-visual-pathway-editor/?model_id=gomodel%3A63f809ec00001779)
+
+![](data:image/png;base64...)
+
+# 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/WIP_-_Regulation_and_Regulatory_Processes_in_GO-CAM.md

@@ -0,0 +1,31 @@
+# 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](https://amigo.geneontology.org/amigo/term/GO%3A0009298)), 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)](http://noctua.geneontology.org/workbench/noctua-visual-pathway-editor/?model_id=gomodel%3A662af8fa00000838).
+
+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 GDP-alpha-D-mannose (2-), Gmppa undergoes a conformational change that then inhibits catalytic activity of Gmppb.
+
+![](data:image/png;base64...)
+
+https://www.nature.com/articles/s41594-021-00591-9
+
+![](data:image/png;base64...)

aurelian/agents/gocam/documents/md/DNA-binding_transcription_factor_activity_annotation_guidelines.md

@@ -0,0 +1,131 @@
+Guidelines for DNA-binding transcription factor
+annotation in eukaryotes
+Pathway Editor
+DNA-binding transcription factor activity - Single transcription target
+The activity unit for a eukaryotic DNA-binding transcription factor is:
+o MF: 'enables' a child of DNA binding transcription factor activity, RNA polymerase, IIspecific (GO:0000981):
+▪
+
+DNA-binding transcription activator activity, RNA polymerase, II-specific
+(GO:0001228)
+
+▪
+
+DNA-binding transcription repressor activity, RNA polymerase II-specific
+(GO:0001227)
+
+o
+
+Context:
+▪
+
+The relation between the DNA-binding transcription factor activity and the
+gene it regulates is 'has input'
+
+▪
+
+BP: 'part of' regulation of the BP in which the target participates (if known).
+
+▪
+
+CC: 'occurs in' nucleus (GO:0005634)
+
+▪
+
+The causal relation between the transcription factor activity and the activity of
+its target gene is: ‘indirectly positively regulates’ or 'indirectly negatively
+regulates’, since there are many steps between the activation of transcription
+and the activity of the target protein, including the production of a messenger
+RNA that is translated into a protein, i. e the regulator does not directly
+interact with the protein it regulates.
+
+Example single target: FOXO3 regulation of G6PC1
+
+DNA-binding transcription factor activity - Multiple transcription targets
+In cases where transcription factor regulates multiple target genes, a separate activity unit is
+captured for each transcriptional target.
+
+Example multiple targets: FOXO3 regulation of G6PC1 and Pck1
+
+Nuclear receptors and ligand-activated transcription factors
+●
+
+Nuclear receptors are positively regulated by a ligand, usually a small molecule
+(ChEBI).
+
+●
+
+The activity unit for a nuclear receptor is:
+○ MF: nuclear receptor activity (GO:0004879) (a child of transcription factor
+activity)
+○ Context: the causal relation between the small molecule and the nuclear
+receptor is ‘is small activator of’.
+○ Other data are captured the same way as for other transcription factors.
+
+Example: Model for nuclear receptor annotation
+
+Form Editor
+DNA-binding transcription factor activity
+o
+
+MF: 'enables' a child of DNA binding transcription factor activity, RNA polymerase, IIspecific (GO:0000981):
+▪
+
+DNA-binding transcription activator activity, RNA polymerase, II-specific
+(GO:0001228)
+
+▪
+
+DNA-binding transcription repressor activity, RNA polymerase II-specific
+(GO:0001227)
+
+o
+
+Context:
+▪
+
+The relation between the DNA-binding transcription factor activity and the
+gene it regulates is 'has input'. A single input is captured per activity unit.
+
+▪
+
+regulation of transcription may be 'part of' a larger BP, specifically,
+regulation of the BP in which the target participates (if known).
+
+▪
+
+CC: 'occurs in' nucleus (GO:0005634)
+
+Example DNA binding transcription factor activity: FOXO3 regulation of G6PC1
+
+Nuclear receptors and ligand-activated transcription factors
+Example: Model for nuclear receptor annotation guidelines
+The annotations are the same as for DNA binding transcription factor activity, except using
+the more precise MF nuclear receptor activity (GO:0004879).
+
+Differences between GO-CAM and standard
+annotation of a DNA-binding transcription factor
+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 DNA binding
+transcription factor and the MF of its transcriptional target.
+For nuclear receptors, the relation between the small molecule activator and the transcription
+factor is not captured.
+
+Open questions
+-
+
+FORM: For nuclear receptors, the relation between the small molecule activator and
+the transcription factor is not captured: can we add the relation in the Form?
+
+Future features
+Chromosomal coordinates of the promoter/enhancer/loop anchor binding site of a DNAbinding transcription factor will be captured as 'has input'. For for the human genome, the
+syntax is: hg38_chr6:12334566-12335555* if we want to capture the chromosomal region
+
+* https://eu.idtdna.com/pages/support/faqs/how-are-genomic-coordinates-defined
+
+Review information
+Review date: 2023-07-20
+Reviewed by: Cristina Casals, Pascale Gaudet, Patrick Masson
+
+

aurelian/agents/gocam/documents/md/E3_ubiquitin_ligases.md

@@ -0,0 +1,166 @@
+E3 ubiquitin ligases
+An E3 ubiquitin ligase is a protein that recruits an E2 ubiquitin-conjugating enzyme loaded
+with ubiquitin, recognizes a protein substrate, and assists or directly catalyzes the transfer of
+ubiquitin from the E2 to the protein substrate.
+The recognition of the protein substrate can be done by the ubiquitin protein ligase itself or
+through a complex composed of ubiquitin ligase-substrate adaptor and ubiquitin ligase
+complex scaffolds.
+https://en.wikipedia.org/wiki/Ubiquitin_ligase
+
+How to annotate E3 ubiquitin ligases
+E3 ligase that promotes ubiquitination by itself
+The molecular activity unit for the ubiquitin ligase is:
+○ MF: 'enables' ubiquitin protein ligase activity GO:0061630
+○ 'has input' the substrate protein
+○ BPs:
+○ 'part of' ubiquitination (GO:0016567): if known, the BP should describe the
+type of ubiquitination (K-48, K-63…)
+ex: protein K48-linked ubiquitination GO:0070936; otherwise, use the parent protein
+ubiquitination GO:0016567 or protein polyubiquitination GO:0000209.
+● the ubiquitination is part_of the biological process in which the ubiquitination
+is involved:
+e. g. : proteasome-mediated ubiquitin-dependent protein catabolic process
+GO:0043161 or children, such as: SCF-dependent proteasomal ubiquitindependent protein catabolic process (GO:0031146) or ubiquitin-dependent
+protein catabolic process via the C-end degron rule pathway (GO:0140627)
+● and/or part of’ the BP in which the ubiquitination is involved: DNA repair, DNA
+damage response, lysosomal degradation, etc
+regulated by this mechanism (ex: negative regulation of inflammatory
+response, GO:0050728)
+● The causal relation to the substrate molecular activity unit is: ‘indirectly negatively
+regulates’.
+
+Example: TRIM45-mediated degradation of TAB2 leading to inflammatory response
+inhibition (Human)
+
+An E3-ligase complex with adaptors and scaffold protein(s)
+●
+
+The molecular activity unit for the ubiquitin ligase complex scaffold, such as CUL4A
+and/or DDB1 is:
+○ MF: ubiquitin ligase complex scaffold activity GO:0160072
+○ Has input both the ubiquitin ligase-substrate adaptor and the ubiquitin protein
+ligase
+○ BP: if known, the BP should describe the type of ubiquitination (K-48, K-63…)
+ex: protein K48-linked ubiquitination GO:0070936
+if not known, use a BP describing the biological process in which the
+ubiquitination is involved in.
+ex: proteasome-mediated ubiquitin-dependent protein catabolic process
+GO:0043161 or children, such as: SCF-dependent proteasomal ubiquitindependent protein catabolic process (GO:0031146) or ubiquitin-dependent
+protein catabolic process via the C-end degron rule pathway (GO:0140627)
+‘Part of’ the BP regulated by this mechanism (ex: T cell activation,
+GO:0042110)
+
+●
+
+The causal relation between the substrate molecular activity unit is: ‘directly
+negatively regulates’ if it leads to degradation. (to decide for the other cases)
+
+●
+
+The causal relation to the ubiquitin ligase-substrate adaptor molecular activity unit is:
+‘directly regulates’.
+
+●
+
+The molecular activity unit for the ubiquitin ligase-substrate adaptor is:
+○ MF: ubiquitin ligase-substrate adaptor activity GO:1990756
+○ Has input the substrate protein
+○ BP: if known, the BP should describe the type of ubiquitination (K-48, K-63…)
+ex: protein K48-linked ubiquitination GO:0070936
+if not known, use a BP describing the biological process in which the
+ubiquitination is involved in.
+ex: proteasome-mediated ubiquitin-dependent protein catabolic process
+GO:0043161 or children, such as: SCF-dependent proteasomal ubiquitin-
+
+dependent protein catabolic process (GO:0031146) or ubiquitin-dependent
+protein catabolic process via the C-end degron rule pathway (GO:0140627)
+‘Part of’ the BP regulated by this mechanism (ex: T cell activation,
+GO:0042110)
+●
+
+The causal relation to the ubiquitin ligase molecular activity unit is: ‘directly provides
+input for’.
+
+●
+
+Annotation of the ubiquitin ligase is the same as above
+
+Example: DCAF12 controls MOV10 during T cell activation. (Human)
+
+When only substrate adaptor and substrate are known (scaffold and ligase not
+known)
+
+Example: FBXL19-mediated degradation of IL1R1 via GSK3B (Human)
+
+●
+
+The molecular activity unit for the ubiquitin ligase-substrate adaptor is:
+○ MF: ubiquitin ligase-substrate adaptor activity GO:1990756
+○ Has input the substrate protein
+○ BP: if known, the BP should describe the type of ubiquitination (K-48, K-63…)
+ex: protein K48-linked ubiquitination GO:0070936
+
+if not known, use a BP describing the biological process in which the
+ubiquitination is involved in.
+ex: proteasome-mediated ubiquitin-dependent protein catabolic process
+GO:0043161 or children, such as: SCF-dependent proteasomal ubiquitindependent protein catabolic process (GO:0031146) or ubiquitin-dependent
+protein catabolic process via the C-end degron rule pathway (GO:0140627)
+‘Part of’ the BP regulated by this mechanism (ex: T cell activation,
+GO:0042110)
+●
+
+The causal relation to the substrate molecular activity unit is: ‘indirectly regulates’
+since we don’t add/have information about the E3 ligase.
+
+When only substrate adaptor, scaffold and substrate are known (ligase not known)
+Ex: DCAF13 supports the spindle assembly and chromosome condensation during oocyte
+meiotic division by targeting PTEN polyubiquitination and degradation. (Human)
+
+●
+
+●
+●
+
+The molecular activity unit for the ubiquitin ligase complex scaffold, such as CUL4A
+and/or DDB1 is:
+○ MF: ubiquitin ligase complex scaffold activity GO:0160072
+○ Has input both the ubiquitin ligase-substrate adaptor and the ubiquitin protein
+ligase
+○ BP: if known, the BP should describe the type of ubiquitination (K-48, K-63…)
+ex: protein K48-linked ubiquitination GO:0070936
+if not known, use a BP describing the biological process in which the
+ubiquitination is involved in.
+ex: proteasome-mediated ubiquitin-dependent protein catabolic process
+GO:0043161 or children, such as: SCF-dependent proteasomal ubiquitindependent protein catabolic process (GO:0031146) or ubiquitin-dependent
+protein catabolic process via the C-end degron rule pathway (GO:0140627)
+‘Part of’ the BP regulated by this mechanism (ex: T cell activation,
+GO:0042110)
+The causal relation to the ubiquitin ligase-substrate adaptor molecular activity unit is:
+‘directly regulates’.
+The molecular activity unit for the ubiquitin ligase-substrate adaptor is:
+○ MF: ubiquitin ligase-substrate adaptor activity GO:1990756
+○ Has input the substrate protein
+○ BP: if known, the BP should describe the type of ubiquitination (K-48, K-63…)
+ex: protein K48-linked ubiquitination GO:0070936
+if not known, use a BP describing the biological process in which the
+ubiquitination is involved in.
+
+ex: proteasome-mediated ubiquitin-dependent protein catabolic process
+GO:0043161 or children, such as: SCF-dependent proteasomal ubiquitindependent protein catabolic process (GO:0031146) or ubiquitin-dependent
+protein catabolic process via the C-end degron rule pathway (GO:0140627)
+‘Part of’ the BP regulated by this mechanism (ex: T cell activation,
+GO:0042110)
+●
+
+The causal relation to the substrate molecular activity unit is: ‘indirectly regulates’
+since we don’t add/have information about the E3 ligase.
+
+Examples of larger processes in which various types of
+ubiquitination play a role
+
+Source: PMID:27285106
+
+Review date:
+Reviewed by:
+
+

aurelian/agents/gocam/documents/md/GO-CAM_annotation_guidelines_README.md

@@ -0,0 +1 @@
+

aurelian/agents/gocam/documents/md/GO-CAM_modelling_guidelines_TO_DO.md

@@ -0,0 +1,5 @@
+Moved here.
+https://docs.google.com/document/d/
+13MWyxdfcS78dYz9hg61R4ZS4ydp3OY8Y16LAb3xD3Ug/edit#
+
+

aurelian/agents/gocam/documents/md/How_to_annotate_complexes_in_GO-CAM.md

@@ -0,0 +1,28 @@
+How to annotate complexes in GO-CAM
+When complexes are involved in specific activities, several options are available in GO-CAM
+to represent them.
+
+1- The subunit that carries the molecular activity is known:
+In that case, the complex is not described and the activity(ies) is represented by the specific
+protein (s) carrying the activity.
+Ex:
+
+In this example, all the proteins in the E3 ligase complex have a defined and precise activity.
+Therefore, they are all displayed in the model. In this case, the scaffold activity is usually
+represented first, activating subsequent activities from the complex.
+
+2- The subunit which carries the molecular activity is not known:
+
+If the precise subunit carrying the activity is not known, we can use the GO accession for the
+complex.
+Ex: Ragulator complex (GO:0071986): Ragulator is comprised of the membrane anchor
+subunit LAMTOR1, LAMTOR2, LAMTOR3, LAMTOR4 and LAMTOR5.
+
+In this example LAMTOR1 activity is known (protein-membrane adaptor activity) but the
+protein that carries the guanyl-nucleotide exchange factor activity is not known, therefore we
+use the complex ID from GO in this situation.
+
+3- If the activity is shared by several proteins
+EX: Heterodimeric receptor where both activities are important for activity.
+
+

aurelian/agents/gocam/documents/md/How_to_annotate_molecular_adaptors.md

@@ -0,0 +1,19 @@
+How to annotate molecular adaptors
+Here we describe how to capture a molecular adaptor activity which is defined as the binding
+activity of a molecule that brings together two or more molecules through a selective, noncovalent, often stoichiometric interaction, permitting those molecules to function in a
+coordinated way.
+Example 1: TYROBP acts as an adaptor between a receptor and a downstream effector
+
+The molecular activity unit for molecular adaptor may include:
+o MF: molecular adaptor activity (GO:0060090) or one of its children
+o Has input the two (or more) molecules it brings together.
+o BP: the BP it participates in
+o CC: the place where the activity occurs.
+The relation with the downstream activity used is “directly positively regulates”
+
+Example 2: When an adaptor brings together an enzyme and its substrate
+
+The molecular activity is the same as above (MF, inputs, BP, CC)
+But in that case, the relation with the downstream activity used is “provides input for”
+
+

aurelian/agents/gocam/documents/md/How_to_annotate_sequestering_proteins.md

@@ -0,0 +1,38 @@
+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 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: the BP it inhibits
+○ CC: the place where the activity occurs.
+●
+○ The causal relation between the sequestering activity and the activity of the
+protein it inhibits is 'directly positively regulates'.
+
+Example 1: Sequestering activity of CAV1 on TLR4 signaling
+
+The molecular activity unit for molecular adaptor may include:
+o MF: molecular sequestering activity (GO:0140313) or one of its children
+o
+The relation with the downstream activity used is “directly negatively regulates”
+
+Example 2: Sequestering activity of YWHAZ on RAF1
+
+In that example, the difference in the cellular component between the two activities clearly
+show that the YWHAZ protein sequesters RAF1 in the cytoplasm, preventing its activity in
+the plasma membrane.
+The relation used between both activities is “directly negatively regulates” because there
+is direct interaction between both proteins.
+
+Form Editor
+
+Review date: 2023-06-22
+Reviewed by: Pascale Gaudet, Patrick Masson
+
+

aurelian/agents/gocam/documents/md/Molecular_adaptor_activity.md

@@ -0,0 +1,52 @@
+Guidelines for annotating molecular adaptor
+activity
+A molecular adaptor activity is the binding activity of a molecule that brings together two or
+more molecules through a selective, non-covalent, often stoichiometric interaction, permitting
+those molecules to function in a coordinated way.
+
+Pathway Editor
+The molecular activity unit for a molecular adaptor is:
+●
+●
+
+MF: 'enables' molecular adaptor activity (GO:0060090) or a child
+Context:
+○ The relation between the adaptor activity and the two (or more) molecules it
+brings together is 'has input'
+○ BP: 'part of' the BP in which the adaptor participates
+○ CC: 'occurs in' the cellular location where the activity takes place.
+
+The relation between the adaptor and the proteins it adapts can be 'directly positively
+regulates' or 'provides input for', depending if the activity of the adaptor is regulatory.
+Example 1: TYROBP acts as an adaptor between a receptor and a downstream
+effector
+SIGLEC1 recognizes and endocytoses virions, which leads to activation of the TYROBP
+molecular adaptor, which recruits PTPN11. The scaffolding activity of PTPN11 is activated
+by TYROBP.
+
+Example 2: An adaptor that brings together an enzyme and its substrate
+
+In that case, the relation between the adaptor activity and the downstream activity is
+'provides input for'.
+
+Form Editor
+●
+●
+
+MF: 'enables' molecular adaptor activity (GO:0060090) or a child
+Context:
+○ The relation between the adaptor activity and the two (or more) molecules it
+brings together is 'has input'
+○ BP: 'part of' the BP in which the adaptor participates
+○ CC: 'occurs in' the cellular location where the activity takes place.
+
+Differences between GO-CAM and standard
+annotation of a molecular adaptor activity
+In standard annotation (captured with the Noctua Form or Protein2GO), relations between
+molecular functions are not captured.
+
+Review information
+Review date: 2023-07-20
+Reviewed by: Cristina Casals, Pascale Gaudet, Patrick Masson
+
+

aurelian/agents/gocam/documents/md/Molecular_carrier_activity.md

@@ -0,0 +1,59 @@
+Guidelines for annotating molecular carrier activity
+Pathway Editor
+The activity unit for a molecular carrier is:
+●
+
+MF: a molecular carrier 'enables' molecular carrier activity (GO:0140104) or a child
+
+●
+
+Context:
+o
+
+o
+
+o
+
+The relation between a transported molecule and its carrier is 'has input'. The
+carrier and the small molecule are linked with the 'has output' relation, so that the
+small molecule can be the input for the next reaction.
+BP 'part of' the process in the molecule using the small molecule participates, or
+'part of' regulation of the process, if the carrier is regulators (rate-limiting for the
+execution of the process)
+CC: 'occurs in' the cellular location where the activity takes place.
+
+Example 1: LPS is carried to its receptor by CD14
+
+Form Editor
+The activity unit for a molecular carrier is:
+●
+
+MF: a molecular carrier 'enables' molecular carrier activity (GO:0140104) or a child
+
+●
+
+Context:
+o
+
+o
+
+o
+
+The relation between a transported molecule and its carrier is 'has input'. The
+carrier and the small molecule are linked with the 'has output' relation, so that the
+small molecule can be the input for the next reaction.
+BP 'part of' the process in the molecule using the small molecule participates, or
+'part of' regulation of the process, if the carrier is regulators (rate-limiting for the
+execution of the process)
+CC: 'occurs in' the cellular location where the activity takes place.
+
+Differences between GO-CAM and standard
+annotation for a molecular carrier activity
+The same information is captured for the carrier activity and its context; however in the standard
+annotations,it is not possible to capture the order of the reactions.
+
+Review information
+Review date: 2023-07-25
+Reviewed by: Cristina Casals, Pasclae Gaudet, Patrick Masson
+
+