Metabolic

Pathways where series of reactions depict the conversion of molecules as controlled by enzymes and release or use of energy. These pathways elucidate how biomolecules are synthesized (anabolism) and broken down (catabolism) to support energy production and cellular processes. General examples include glycolysis and the citric acid cycle. Understanding these pathways is a key to grasping how the body extracts energy, synthesizes essential molecules, and maintains metabolic homeostasis, with profound implications for fields ranging from nutrition and biochemistry to medicine and disease research.

NCBO Metabolic Pathway Ontology ID: PW:0000002

Physiological

Pathways are structured sequences of biological events and chemical processes that occur within an organism to regulate and maintain bodily functions. These pathways encompass intricate processes and interactions among cells, tissues, and organs, orchestrating activities like energy production, immune response, and homeostasis whilst showcasing the body’s response to the action of endogenous substances. Understanding physiological pathways is essential for comprehending how the body functions and adapts to various internal and external influences, ensuring overall health and balance.

NCBO Physiological Pathway Ontology ID: PW:0000003, PW:0000004

Signaling

Pathways that show molecular mechanisms in which signals, such as a metabolite, or any other molecule, initiate a series/cascade of events involving multiple molecules, including receptors, proteins, ligands, and messengers. The pathways are situated either upstream or downstream of other signaling pathways, with the primary role of coordinating a broad spectrum of cellular processes. Essentially, these pathways showcase vital communication networks that control and integrate diverse physiological functions.

NCBO Signaling Pathway Ontology ID: PW:0000003

Drug Metabolism

Biochemical reactions within the body involving the use of enzymes and chemical transformation in changing exogenous substances to more active or inactive and/or more suitable state for excretion. Reactions showcase different enzymes, cellular detoxification, and excretion of drug metabolites. Examples include the cytochrome P450 pathway for many drugs. Understanding these pathways is crucial for optimizing drug dosages, predicting drug interactions, and ensuring effective therapeutic outcomes, ultimately influencing biological and pharmaceutical research.

NCBO Drug Metabolism Pathway Ontology ID: PW:0000002

Drug Action

Pathways outline the process by which a drug, administered through various routes, engages with the body at the cellular level to elicit a specific pharmacological response. These pathways elucidate how drugs interact with specific targets, modulate cellular processes, and influence disease pathways. Examples include the beta-adrenergic receptor pathway for cardiovascular drugs. Understanding these pathways is critical for drug development, dosage optimization, and the identification of potential side effects or drug interactions, ultimately improving healthcare and offering insights into the pharmacological basis of treatments for a wide range of conditions.

NCBO Drug Action Pathway Ontology ID: PW:0000754

Disease

Pathways involved in a molecular sequence and small molecule metabolism whereby specific factors or events trigger and contribute to the development and progression of a particular disease condition. These pathways illuminate how imbalances in small molecule metabolism contribute to conditions such as diabetes, lipid disorders, and neurodegenerative diseases. For instance, the insulin signaling pathway is central to diabetes pathogenesis. They offer crucial references for understanding the roles of metabolic dysregulations in disease, guiding research into therapeutic interventions, diagnostics, and lifestyle management for patients, ultimately impacting healthcare and public health.

NCBO Disease Pathway Ontology ID: PW:0000013

Immunological

Intricate cascades of interactions and responses that the immune system uses to detect and combat foreign invaders, such as pathogens and antigens. These pathways encompass various immune cells, proteins signaling molecules, and checkpoints, orchestrating a coordinated defense mechanism mediating different parts of immune responses. General examples include the T-cell receptor signaling pathway and the complement cascade. Understanding these pathways is crucial for deciphering the intricate interplay between the immune system and infections, autoimmune disorders, and immune-related diseases, ultimately advancing immunology, vaccination, and targeted therapies.

NCBO Immunological Pathway Ontology ID: PW:0000023, PW:0002119

Cellular Response

Complex sequences of molecular events within a cell that enable it to react to external stimuli or signals, ensuring proper function and adaptation. These pathways encompass various cellular components, including receptors, signal transducers, and effectors, to initiate specific responses like growth, division, or apoptosis.

NCBO Cellular Response Pathway Ontology ID: PW:0000124, PW:0000648, PW:0002395

Gene Regulatory

Gene regulatory pathways give an overview of the molecular mechanisms that control gene expression. These pathways elucidate how transcription factors, enhancers, and repressors orchestrate the activation or suppression of specific genes. General examples include the Wnt signaling pathway for embryonic development. Understanding these pathways is essential for unraveling how genes are turned on or off, influencing cell differentiation, growth, and responses to environmental cues. This knowledge has significant applications in genetics, developmental biology, and disease research, offering insights into gene regulation's profound impact on various biological processes.

NCBO Gene Regulatory Pathway Ontology ID: PW:0000085, PW:0000181, PW:0000292, PW:0000807, PW:0001068

Growth Factor

The pathways show intricate molecular processes within cells that mediate responses to signaling molecules called growth factors. These coordinated interactions between receptors and downstream molecules show that growth factor pathways play a key role in tissue development, repair, and overall growth, ensuring cells respond appropriately to external cues and maintain tissue integrity.

NCBO Growth Factor Pathway Ontology ID: PW:0000298

Cytokine Signaling

The cytokine signaling pathways are annotated descriptions of molecular interactions initiated by cytokines elucidating how cytokines regulate immune responses, inflammation, and cell communication. These pathways elucidate how cytokines, including interleukins, interferons, and tumor necrosis factor, coordinate responses to infection, inflammation, and cellular communication. For example, the JAK-STAT pathway is central to cytokine signaling. These pathways provide valuable insights into the complex network of signal transduction and molecular events involved in immune system modulation, supporting research in immunology and related fields.

NCBO Cytokine Signaling Pathway Ontology ID: PW:0000828

Protein/Peptide Hormone-Mediated

Protein mediated pathways elucidate the intricate molecular cascades initiated by protein and peptide hormones. These pathways offer comprehensive insights into how these hormones trigger cellular responses, regulating various physiological functions like metabolism, growth, and homeostasis. These pathways elucidate how specific hormones, such as insulin, glucagon, or thyroid hormones, regulate various physiological processes like metabolism. They serve as valuable resources for understanding the nuanced interactions between hormones and their downstream effectors in biological systems.

NCBO Protein/Peptide Hormone-Mediated Pathway Ontology ID: PW:0000511

Neurological Signaling

Neurological signaling pathways describe intricate molecular processes governing communication within the brain and nervous system. These pathways elucidate the orchestration of events and provide detailed insights into the mechanisms that underlie processes including synaptic transmission, neural development, and neurotransmitter biosynthesis and regulation, vital for neurological function. They serve as valuable references for dissecting the complex web of interactions that underpin brain and nervous system activities, facilitating research in neuroscience and related fields.

NCBO Neurological Signaling Pathway Ontology ID: PW:0001251, PW:0000059

Developmental Signaling

Developmental signaling pathways give account of the molecular sequences coordinating the growth, differentiation, and organization of cells and tissues during development. These pathways elucidate the roles of various signaling molecules and receptors in processes like embryogenesis, tissue formation, and organogenesis. They serve as crucial references for understanding the intricate regulatory mechanisms that underlie embryonic development and tissue morphogenesis, facilitating research in developmental biology and related fields.

NCBO Developmental Signaling Pathway Ontology ID: PW:0000650

Kinase Signaling

Kinase signaling pathways show molecular processes initiated by kinases. These pathways elucidate how specific kinases, including MAPK, PI3K, JAK-STAT, EGFR, and AMPK, regulate cell proliferation, differentiation, and survival. They serve as vital references for understanding how kinase-mediated phosphorylation events coordinate diverse cellular responses, playing pivotal roles in cancer, immunity, metabolism, and other biological processes.

NCBO Kinase Signaling Pathway Ontology ID: PW:0001193

Apoptosis Signaling

Apoptosis signaling pathways are series of reactions, molecular mechanisms governing programmed cell death. These pathways elucidate the roles of essential components, including caspases, Bcl-2 family proteins, and death receptors, in the tightly regulated process of cellular self-destruction. Examples encompass pathways triggered by factors like DNA damage, growth factor deprivation, and immune responses, underscoring the significance of apoptosis in maintaining tissue homeostasis and safeguarding against conditions like cancer and neurodegenerative diseases.

NCBO Apoptosis Signaling Pathway Ontology ID: PW:0000275

Stress Activated Signaling

Stress-activated signaling pathways, involve series of reactions and molecular mechanisms that regulate cellular responses to stressors. These pathways elucidate the roles of key components, including kinases like JNK and p38 MAPK, in transmitting stress signals and initiating adaptive or protective responses. General examples include pathways activated in response to oxidative stress, inflammation, or DNA damage. Understanding these pathways is critical for unraveling how cells cope with various stressors, impacting health, aging, and disease processes.

NCBO Stress Activated Signaling Pathway Ontology ID: PW:0000237

Pathogen Activated Signaling

Pathogen-activated signaling pathways are series of reactions that elucidate the roles of critical components, such as Toll-like receptors, NF-kB, and interferon signaling, in orchestrating immune defenses. Examples include pathways activated during viral infections or bacterial challenges or chemokine receptors coupling to the pertussis toxin sensitive Gi proteins among others. Understanding these pathways is vital for unraveling how the immune system recognizes and combats pathogens, shedding light on host-pathogen interactions and guiding the development of treatments and vaccines.

NCBO Pathogen Activated Signaling Pathway Ontology ID: PW:0001028

Transport/Degradation

Transport and degradation pathways provide insight into how cells manage the movement and breakdown of molecules. These pathways elucidate the critical roles of components like transporters, vesicles, lysosomes, and proteasomes in regulating cellular processes. Examples encompass pathways for intracellular protein degradation through the ubiquitin-proteasome system and vesicular transport of substances like neurotransmitters. Understanding these pathways is pivotal for maintaining cellular function, managing waste products, and ensuring the efficient flow of essential molecules, with implications for health, disease, and cellular regulation.

NCBO Transport/Degradation Pathway Ontology ID: PW:0000103

Cytoskeletal Signaling

Cytoskeletal signaling pathways represent the intricate web of molecular interactions governing the cytoskeleton's dynamic and multifaceted roles. These pathways provide details of how essential components, including actin, tubulin, and associated proteins, regulate cellular processes such as cell migration, intracellular transport, and division. General examples include pathways responsible for the formation of lamellipodia or filopodia in cell migration. Understanding these pathways is crucial for appreciating how the cytoskeleton shapes cell structure, supports mechanical functions, and influences various aspects of cell biology, from development to cellular response to external stimuli.

Disease

Disease pathways reveal the intricate interplay between pathogens, proteins, and host cells during infection. These pathways provide a comprehensive overview of the molecular mechanisms involved in various diseases. They elucidate how pathogens manipulate host proteins to establish infection, evade the immune response, and facilitate disease progression. Understanding these pathways is pivotal for identifying potential targets for therapeutic intervention, developing treatments, and gaining insights into host-pathogen interactions, ultimately contributing to improved disease management and prevention.

NCBO Disease Pathway Ontology ID: PW:0000013