IndraLab

Statements


CALM1 binds GO. 48 / 48
| 48

sparser
"Finally, the Gene Ontology Causal Activity Models (GO-CAM, [44]) consists of pathways annotated (manually or computationally) with the Gene Ontology (GO) terminology [45] (i.e. with GO terms describing biological processes, molecular functions and cellular components)."

sparser
"GO-CAM is robust in terms of computational aspects: OWL is a powerful representation that structures knowledge in a way that allows for reasoning and offers the potential for real-time consistency checking during a curation process."

sparser
"GO-CAM is based on the GO terminology and uses the Relation Ontology (RO) terms for the annotation of causal interactions [95]."

sparser
"GO-CAM models center on molecular functions that are part of a biological process, which in turn are part of regulatory or signaling networks."

sparser
"The new GO-CAM curation encourages the annotation of biological pathways, with relations between GO terms added for each step in the pathway (see xref )."

sparser
"For example, the schema includes constraints that define allowable evidence and provenance structures for each assertion within a GO-CAM."

sparser
"Causality between entities in a GO-CAM model is defined via building blocks of the form: ‘a molecular function, enabled by a gene product, regulates a molecular function, enabled by the same or another gene product’."

sparser
"The GO-CAM documentation, data and download are directly accessible through."

sparser
"Current formats of causal statements range from the simplest, with only two entities and the causal relationship [e.g. the Simple Interaction Format (SIF) with ‘A activates B’ or ‘A -> B’], to more complex statements including contextual description [e.g. BEL (Biological Expression Language) ( xref ; xref ), GO-CAM ( xref ) and PSI-MITAB2.8 ( xref )]."

sparser
"We focus on our progress on the curation and public release of GO-CAM models, the continuous collaborative work to refine the GO ontology, the review and improvement of the quality of our annotations, and the expansion of the usability of GO through a redesigned website, documentation, data access, visualization widget and 15 years of historical archives of the GO knowledgebase."

sparser
"We have implemented a computational schema for GO-CAM using ShEx (Shape Expressions), a formal language for describing structures in Resource Description Format (RDF) graphs (), also used in projects such as Wikidata ()."

sparser
"GO-CAM is a strict semantic, descriptive and computable model that enables curators to link together standard GO annotations and enrich them with biological context."

sparser
"GO-CAM repository."

sparser
"Other resources such as GO-CAM and NDEx represent new developments that aim to propel component and network curation results to new future applications and are probably safe for some time to be."

sparser
"These formats can range from the simplest form with two entities and the regulation sign (e.g. SIF) and more complex representations with the storage of additional metadata [e.g. the BEL, GO-CAM using the Web Ontology Language (OWL), and PSI-MITAB]."

sparser
"The biggest change has been in biological process terms, due to refactoring the multi-organism part of the Biological Process branch and the obsoletion of combinatorial terms (e.g. GO:0100052, negative regulation of G1/S transition of mitotic cell cycle by transcription from RNA polymerase II promoter) made up of other GO terms which can now be linked using GO-CAM."

sparser
"The GO-CAM [44] is a formalism developed for structuring biological processes by defining triplets of information (subject, predicate and object) using the OWL representation [94]."

sparser
"26 In addition, we ingest GO-CAM models that capture biological systems such as protein pathways, including those important in SARS-CoV-2 infection."
| DOI

sparser
"The establishment of these guidelines encourages the communities to update data formats (PSI-MITAB2.8, GO-CAM and BEL) and curation protocols to comply with MI2CAST and offer better interoperability between resources supporting these formats."

sparser
"Federated queries allow, for instance, to query features of a GO-CAM and enrich these features with additional information available at other SPARQL endpoints such as UniProt (), identifiers.org () and wikipathway ()."

sparser
"Users will be able to access and merge these data using the MITAB2.8-compliant PSICQUIC webservice ( xref ). xref provides the compliance to MI2CAST of several formats (SIF, PSI-MITAB2.8, BEL and GO-CAM)."

sparser
"These annotations were also deposited in the Gene Ontology annotation repository () as GO-CAM models ( xref )."

sparser
"The new GO-CAM annotation framework was notably improved, and we formalized the model with a computational schema to check and validate the rapidly increasing repository of 2838 GO-CAMs."

sparser
"Still, GO-CAM is mainly based on an activity-level or reaction-level representation of causality rather than an entity-level based causality (even though the latter can be inferred)."

sparser
"Thus, the GO consortium has recently implemented the Gene Ontology Causal Activity Model (GO-CAM; xref ) to allow the representation of comprehensive models of biological pathways."

sparser
"GO-CAM is an extension of the standard GO annotation format that allows more expressive annotations, e.g. specifying the cell type using Cell Ontology terms ( xref ), and multiple pieces of evidence for a single annotation."

sparser
"In theory, PSI-MITAB2.8, BEL and GO-CAM can also be used as input files in modeling tools when the interactions of interest have been selected."

sparser
"SynGO annotations are available as both standard GO annotations () and as GO-CAM models ()."

sparser
"For example, high-throughput experiments for gene expression generate hundreds or sometimes thousands of differentially expressed genes (DEGs), and their associated biological functions can be summarized through enrichment analysis over GO terms. xref Gene-level annotations defined in GO can also be further elaborated into a network of biological pathway annotations via the recently developed GO Causal Activity Modeling (GO-CAM) models to represent the integrative effect of DEGs on the level of biological pathways."

sparser
"We continue to develop Noctua, the new GO curation platform (see GO toolset), to support the curation and review of both standard and GO-CAM annotations."

sparser
"To address this and to help curators, the Noctua annotation platform is being developed (http://noctua.geneontology.org/), providing a graphical user interface for assembling, editing and interpretation of GO-CAM models."

sparser
"GO-CAM in a nutshell."

sparser
"In addition, we ingest GO Causal Activity Models (GO-CAM) models that capture biological systems such as protein pathways, including those important in SARS-CoV-2 infection(Thomas et al., 2019). generate positive edges, a set of positive test edges equal in number to [(1 -train_fraction) * number of edges in input graph] is selected from the edges in the input graph, where train_fraction is a number between 0 and 1 indicating the fraction of the graph to use for training."

sparser
"For example, the Gene Ontology Causal Activity Modeling (GO-CAM) will enable new applications of GO in pathway and network analysis [ xref ]."

sparser
"dictyBase and other curators use a new tool created by the GO consortium (Noctua), to accomplish these GO-CAM annotations."

sparser
"Other resources, such as GO-CAM, focus not on the genes, but on the biological activities of gene products, and represent these activities as being the source and target ‘entities’ of the causal interaction (see Figure 2, Example 2), therefore called ‘activity-based causality’."

sparser
"On the other hand, GO-CAM and BEL allow the representation of causality from an activity-based view for the biological entities, and a process-based view for biological reactions, meaning that the focus is not put on biological entities per se but rather on functions or actions that they can perform."

sparser
"The GO-CAM ShEx schema plus associated documentation is available from."

sparser
"In parallel, the Gene Ontology [GO ( xref )], since 2003, has included a ‘regulation of biological process’ (GO:0050789) branch that has been widely used to annotate causal interactions ( xref ), and has recently been extended into the GO Causal Activity Models (GO-CAM) framework ( xref )."

sparser
"The migrated standard GO annotations are also being checked against the ShEx schema to ensure compliance with the GO-CAM model."

sparser
"In addition, we have initiated a phased project to migrate all standard manual GO annotations generated by Alliance member groups to GO-CAM starting with WormBase ( xref ) and MGI ( xref )."

sparser
"The GO-CAM formalism thus enables queries such as ‘which genes’ activities are upstream or downstream of a given activity or process’ or ‘which genes’ activities directly positively regulate a given activity’."

sparser
"Furthermore, BEL, GO-CAM and PSI-MITAB2.8 allow to depict with precision the biological activities of the entities involved, using GO terms."

sparser
"For storing any type of contextualized causal interactions, the PSI-MITAB2.8, BEL and GO-CAM formats seem to be well suited as they can handle fine-grained details describing a causal interaction."

sparser
"The ongoing “Causal Activity Model” project (GO-CAM; [ xref ]) is going one step further in expressiveness with the design of refined properties between GO-BP and GO-MF."
| PMC

sparser
"Users can now access the GO-CAM repository directly from the GO homepage."

sparser
"In molecular biology, several formalisms (e.g., BEL,87 SBML,182 SBGN,183 BioPAX,184 GO-CAM)185 have the facility to describe the interactions between biological entities that are often elucidated through laboratory or clinical experimentation."

sparser
"MI2CAST considers terms used in formats mentioned previously (e.g. PSI-MITAB2.8, BEL and GO-CAM) and covers the full range of metadata that should ideally be annotated during the curation process to enrich the description of a molecular causal interaction."