Persius/hicric huggingface dataset:
Onyx-15
Onyx 015 is an experimental intratumoral adenovirus, genetically modified from its original cold virus form.
In its unattenuated form, the adenovirus blocks the cell-cycle control protein p53, using the E1B protein, then replicates in the cell it has attacked, and causes lysis, enabling it to spread and infect other cells.
When modified to the Onyx 015 form (E1B-55kDa-deleted), the virus lacks the E1B protein, and so upon infection p53 can block viral replication and initiate cell cycle arrest, and the virus is unable to spread.
However in cancerous cells which lack p53, the virus is still able to replicate. Thus the tumour cells will undergo lysis whilst the healthy surrounding cells are safe.

# Chemotherapeutic Use
Onyx 015 has been used experimentally for combatting head and neck tumours, in combination with the standard chemotherapeutic agents cisplatin and 5-fluorouracil
Opsonin
An opsonin is any molecule that acts as a binding enhancer for the process of phagocytosis, for example, by coating the negatively-charged molecules on the membrane.

# Mechanism
Both the membrane of a phagocytosing cell, as well as its target, have a negative charge (zeta-potential), making it difficult for the two cells to come close together. During the process of opsonization, antigens are bound by antibody and/or complement molecules.  Phagocytic cells express receptors that bind opsonin molecules. These include the Fc receptors.  With the antigen coated in these molecules, binding of the antigen to the phagocyte is greatly enhanced.  Most phagocytic binding cannot occur without opsonization of the antigen.
Furthermore, opsonization of the antigen and subsequent binding to an activated phagocyte will cause increased expression of complement receptors on neighboring phagocytes.

# Examples
Examples of opsonin molecules include:
- antibodies: IgG and IgA
- components of the complement system: C3b, C4b, and iC3b
- Surfactant
- Mannose-binding lectin (initiates the formation of C3b)
The most important are IgG and C3b.
Oxalate

# Overview
An oxalate (also ethanedioate) is a salt or ester of oxalic acid. As a salt, the oxalate anion has the chemical formula C2O42 or (COO)22.
Consumption of oxalates (for example, the grazing of animals on oxalate-containing plants such as greasewood), or human consumption of Sorrel may result in kidney disease or even death due to oxalate poisoning.
The charge on oxalate allows it to act as a chelator of various positively charged metal ions.
Much of its other properties resemble oxalic acid.

# Examples
- sodium oxalate - Na2C2O4
- calcium oxalate - CaC2O4, a major component of kidney stones
- dimethyl oxalate - (CH3)2C2O4
- phenyl oxalate ester - (C6H5)2C2O4
- potassium ferrioxalate - , an iron complex with oxalate ligands
- ammonium oxalate - (NH4)2C2O4
Oxoacid

# Overview
An oxoacid is an acid which contains oxygen. More specifically, it is an acid which:
- contains oxygen;
- contains at least one other element;
- has at least one hydrogen atom bound to oxygen; and
- forms an ion by the loss of one or more protons.
The name oxyacid is sometimes used, although this is not recommended.
Generally, oxoacids are simply polyatomic ions with a hydrogen cation.
Under Lavoisier's original theory, all acids contained oxygen, which was named from the Greek  (oxys) (acid, sharp) and  (geinomai) (engender). It was later discovered that some acids, notably hydrochloric acid, did not contain oxygen and so a distinction was made for those that did.
Common oxoacids include:
- Halogen oxoacids: Hypochlorous acid; Chlorous acid; Chloric acid; Perchloric acid; Perbromic acid; Metaperiodic acid
- Sulfuric acid
- Nitric acid
- Phosphoric acid
Common acids which are not oxoacids include:
- Hydrochloric acid
- Hydrofluoric acid
- Hydrobromic acid
- Hydroiodic acid
Although carboxylic acids fulfill the criteria above, they are not generally considered as oxoacids.
All oxoacids have the acidic hydrogen bound to an oxygen atom, so bond strength (length) is not a factor as it is with binary nonmetal hydrides. Rather, the electronegativity of the central atom (E) and the number of O atoms determine oxoacid acidity. With the same number of oxygens around E, acid strength increases with the electronegativity of E.

# Note
- ^  This final criterion has the effect of excluding boric acid from the strict definition, as it forms its anion by addition of hydroxide rather than loss of a proton: B(OH)3 + H2O   + H+. However, boric acid is usually considered to be an oxoacid nonetheless.
Oxydose
Oxydose
AHX'-e-dose (proper noun)
1. Oxydose is a liquid opioid narcotic elixir. Its active ingredient is oxycodone hydrochloride U.S.P., a U.S. Schedule II opioid. It is prescribed for severe pain, where immediate pain relief is required, sometimes relieving intractable pain in up to five minutes when used sublingually. Oxycodone Hydrochloride is also used in other preparations such as Percocet Roxicodone and other prescription pain killers. Oxydose is highly concentrated in a vanilla & grape flavored liquid vehicle containing 20mg/ml. Oxydose is currently manufactured by Ethex Pharmaceuticals.
Oxycodone, like most opioids has a potential for abuse and dependence and therefore may be habit-forming.
see also, OxyFast C-II (oxycodone HCl immediate-release) Oral Concentrate Solution (the Brand name equivalent for Oxydose, a registered trademark of Purdue Pharma)
Ozonide
Ozonide is an unstable, reactive polyatomic anion O3, derived from ozone, or an organic compound similar to organic peroxide formed by a reaction of ozone with an unsaturated compound.

# Inorganic ozonides
Inorganic ozonides are dark red ionic compounds containing the reactive O3 anion. The anion has the V shape of the ozone molecule.
Inorganic ozonides are formed by burning potassium or heavier alkali metals in ozone, or by treating the alkali metal hydroxide with ozone; if potassium is left undisturbed in air for years it accumulates a covering of superoxide and ozonide. They are very sensitive explosives that have to be handled at low temperatures in an atmosphere comprised of an inert gas. Lithium and sodium ozonide are extremely unstable and must be prepared by low-temperature ion exchange starting from CsO3, and the pure solids cannot be isolated.
Inorganic ozonides are being investigated as promising sources of oxygen in chemical oxygen generators.

# Organic ozonides
Organic ozonides are more explosive cousins of the organic peroxides and contain a covalently bonded ozonide group, -O-O-O-. They usually appear in the form of foul-smelling oily liquids. Their main use is in determining the structure of chemical compounds. As intermediates of ozonolysis, they are formed by an addition reaction of ozone and unsaturated compounds, and rapidly decompose to carbonyl compounds - aldehydes, ketones, peroxides.
PCDH11X
Protocadherin 11 X-linked, also known as PCDH11X, is a protein which in humans is encoded by the PCDH11X gene.

# Function
This gene belongs to the protocadherin gene family, a subfamily of the cadherin superfamily. The encoded protein consists of an extracellular domain containing 7 cadherin repeats, a transmembrane domain and a cytoplasmic tail that differs from those of the classical cadherins. The gene is located in a major X/Y block of homology and its Y homolog (PCDHY), despite divergence leading to coding region changes, is the most closely related cadherin family member. The protein is thought to play a fundamental role in cellcell recognition essential for the segmental development and function of the central nervous system. Transcripts arising from alternative splicing encode isoforms with variable cytoplasmic domains.

# Clinical significance
In a genome-wide association study, the PCDH11X gene has been linked as a risk factor in late onset Alzheimer's disease, but other studies on different populations  could not confirm the initial association. The clinical significance of this gene is unclear, and the gene might play different roles in different population specific contexts.
PDBWiki
PDBWiki is a user contributed database of protein structure annotations, listing all the protein structures currently available in the Protein Data Bank (PDB). The aims of PDBWiki, focusing on user contributed annotation and classification, have been met by the use of the MediaWiki software system, making PDBWiki a 'Wiki-Database'. 

# Motivation
The Protein Data Bank (PDB) is the central archive of experimentally solved biomolecular structures. However, the PDB only allows data retrieval and does not provide functionality for collaboration or user feedback. In contrast, PDBWiki is a website for sharing expert knowledge about structures deposited in the PDB. Using the same MediaWiki system underlying Wikipedia] it provides online tools for discussing and annotating proteins in a collaborative way. The goal is to create a central and freely accessible repository of user-contributed information that will be useful for anyone working with PDB structures. As such PDBWiki can be considered a part of a wider effort in community-based biological databases curation. 

# Database content
Currently PDBWiki contains details of more than 50,000 protein structures and over 50 'user-contributed' annotations, making it a significant resource for the structural biology community.

# About
PDBWiki was developed as part of the BioWiki initiative, and was entered into the third International Openfree Bioinformation Contents Competition organised by BiO.CC, the top level biological information web site operated by KOBIC.
PEG 400
PEG 400 (Polyethylene Glycol 400) is a low molecular weight grade of Polyethylene glycol. It is a clear, colorless, viscous liqid.  Due in part to its low toxicity, PEG 400 is widely used in a variety of pharmaceutical formulations.

# Additional Properties
PEG 400 is strongly hydrophilic.  The partition coefficient of polyethylene glycol 414 between hexane and water is 0.000015 (log P = -4.8), indicating that when polyethylene glycol 414 is mixed with water and hexane, there are only 1.5 parts of polyethylene glycol 414 in the hexane layer per 100,000 parts of polyethylene glycol 414 in the water layer.
PEG 400 is soluble in water, acetone, alcohols, benzene, glycerin, glycols, aromatic hydrocarbons and is slightly soluble in aliphatic hydrocarbons.
PIP4K2A
Phosphatidylinositol-5-phosphate 4-kinase type-2 alpha is an enzyme that in humans is encoded by the PIP4K2A gene.

# Function
Phosphatidylinositol-4,5-bisphosphate, the precursor to second messengers of the phosphoinositide signal transduction pathways, is thought to be involved in the regulation of secretion, cell proliferation, differentiation, and motility. The protein encoded by this gene is one of a family of enzymes capable of catalyzing the phosphorylation of phosphatidylinositol-4-phosphate on the fifth hydroxyl of the myo-inositol ring to form phosphatidylinositol-4,5-bisphosphate. The amino acid sequence of this enzyme does not show homology to other kinases, but the recombinant protein does exhibit kinase activity. This gene is a member of the phosphatidylinositol-4-phosphate 5-kinase family.

# Clinical Importance
Through genome wide association studies (GWAS), some of the single nucleotide polymorphisms (SNPs) located in this gene have been noticed to be significantly associated with susceptibility of childhood acute lymphoblastic leukaemia in ethnically diverse populations.
PIP4K2B
Phosphatidylinositol-5-phosphate 4-kinase type-2 beta is an enzyme that in humans is encoded by the PIP4K2B gene.
The protein encoded by this gene catalyzes the phosphorylation of phosphatidylinositol-4-phosphate on the fifth hydroxyl of the myo-inositol ring to form phosphatidylinositol-4,5-bisphosphate. This gene is a member of the phosphatidylinositol-4-phosphate 5-kinase family. The encoded protein sequence does not show similarity to other kinases, but the protein does exhibit kinase activity. Additionally, the encoded protein interacts with p55 TNF receptor.

# Interactions
PIP4K2B has been shown to interact with TNFRSF1A. In addition, PIP4K2B has been shown to interact with PIP4K2A and may modulate the cellular localisation of PIP4K2A.

# Structure
The structure of PIP4K2B has been determined through X-ray crystallography.
PIP5K1C
Phosphatidylinositol-4-phosphate 5-kinase type-1 gamma is an enzyme that in humans is encoded by the PIP5K1C gene.
This gene encodes a member of the type I phosphatidylinositol-4-phosphate 5-kinase family of enzymes. A similar protein in mice is found in synapses and focal adhesion plaques, and binds the FERM domain of talin through its C-terminus.

# Model organisms
Model organisms have been used in the study of PIP5K1C function. A conditional knockout mouse line, called Pip5k1ctm1a(KOMP)Wtsi was generated as part of the International Knockout Mouse Consortium program  a high-throughput mutagenesis project to generate and distribute animal models of disease to interested scientists.
Male and female animals underwent a standardized phenotypic screen to determine the effects of deletion. Twenty three tests were carried out on mutant mice and two significant abnormalities were observed. Fewer than expected homozygous mutant embryos were identified during gestation, and none survived until weaning. The remaining tests were carried out on heterozygous mutant adult mice and no further phenotypes were observed.
PITPNM1
Membrane-associated phosphatidylinositol transfer protein 1 is a protein that in humans is encoded by the PITPNM1 gene.

# Function
PITPNM1 belongs to a family of proteins that share homology with the Drosophila retinal degeneration B (rdgB) protein.
It was found that aggressive metastasized cancer cells produced more of the PITPNC1 protein. In contrast, tumor cells that had not spread had lower expression of PITPNC1. Studies reveal that PITPNC1 promotes malignant secretion by binding Golgi-resident PI4P and localizing RAB1B to the Golgi. RAB1B localization to the Golgi allows for the recruitment of GOLPH3 (Golgi phosphoprotein 3), which facilitates Golgi extension and enhanced vesicular release. PITPNC1-mediated vesicular release drives metastasis by increasing the secretion of pro-invasive and pro-angiogenic mediators HTRA1, MMP1, FAM3C, PDGFA, and ADAM10.

# Interactions
PITPNM1 has been shown to interact with PTK2B.
PLA2G4A
Cytosolic phospholipase A2 is an enzyme that in humans is encoded by the PLA2G4A gene.

# Function
This gene encodes a member of the cytosolic phospholipase A2 group IV family. The enzyme catalyzes the hydrolysis of membrane phospholipids to release arachidonic acid which is subsequently metabolized into eicosanoids. Eicosanoids, including prostaglandins and leukotrienes, are lipid-based cellular hormones that regulate hemodynamics, inflammatory responses, and other intracellular pathways. The hydrolysis reaction also produces lysophospholipids that are converted into platelet-activating factor. The enzyme is activated by increased intracellular Ca2+ levels and phosphorylation, resulting in its translocation from the cytosol and nucleus to perinuclear membrane vesicles.

# Interactions
PLA2G4A has been shown to interact with HTATIP.

# Clinical significance
Mutations in this gene have been associated with multifocal stenosing ulceration of the small intestine.
PLEKHG5
Pleckstrin homology domain containing, family G member 5 (PLEKHG5) is a protein that in humans is encoded by the PLEKHG5 gene. Multiple transcript variants encoding different isoforms have been found for this gene.

# Function
This gene encodes a protein that activates the nuclear factor kappa B (NFKB1) signaling pathway.

# Clinical significance
Mutations in the PLEKHG5 gene are associated with distal spinal muscular atrophy type 4.
PLEKHM2
Pleckstrin homology domain-containing family M member 2 is a protein that in humans is encoded by the PLEKHM2 gene.

# Model organisms
Model organisms have been used in the study of PLEKHM2 function. A conditional knockout mouse line, called Plekhm2tm1a(EUCOMM)Wtsi was generated as part of the International Knockout Mouse Consortium programa high-throughput mutagenesis project to generate and distribute animal models of disease to interested scientists.
Male and female animals underwent a standardized phenotypic screen to determine the effects of deletion. Twenty six tests were carried out on mutant mice and three significant abnormalities were observed. Male homozygous mutants had increased circulating alkaline phosphatase levels and an increased susceptibility to bacterial infection, while females had an increased leukocyte cell number.
PLEKHM3
Pleckstrin Homology domain containing Family  M Member 3, or PLEKHM3, is the hypothetical protein that in humans is encoded by the PLEKHM3 gene. PLEKHM3 is also known as DAPR (differentiation associated protein),  and Pleckstrin Homology Domain Containing Family M, Member 1-like.

# Gene
PLEKHM3 is a valid, protein coding gene that is located on the minus strand of the q-arm of chromosome 2. Its exact location is 2q33.3. Its genomic mRNA length is 9,807 base pairs.
Its genomic DNA length is 24.3 kilobases. It has 8 exons, 4 common splice forms.

# Protein
PLEKHM3 contains 3 domains. Two domains are highly conserved across mammalian species. The most highly conserved region is the DUF4206 Domain. The third is a domain of unknown function 4206, which is highly conserved across all eukarya. Its molecular weight is 87.2 kilodaltons. Its isoelectric point is 6.81. It is predicted to be localized primarily in the cytosol. PLEKHM3 has orthologs in eukaryotes.

## Function
The function of PLEKHM3 is not characterized in any scientific database. It is thought to be associated with cell differentiation and is expressed at ubiquitously low levels in all cell types. The Pleckstrin Homology domains are involved with phosphate binding. The DUF4206 Domain is cysteine rich and forms with 7 CXXC protein motifs. This motif is responsible for forming disulfide bridges. The DUF4206 domain is conserved in PLEKHM3 homologs as distant as Nile Tilapia.

## Interactions
PLEKHM3 is thought to interact with a protein called GDAP1, which is responsible for differentiation in neuronal cell types and plays a role in the signal transduction pathway. This also supports the predicted role of PLEKHM3 in differentiation.
PLXNA4A
Plexin-A4 is a protein that in humans is encoded by the PLXNA4 gene.

# Function
Plexin A4 binds to neuropilin 1 (Nrp1) and neuropilin 2 (Nrp2) and transduces signals from Sema3A, Sema6A, and Sema6B. These Nrp-plexin and semaphorin complexes initiate cascades that regulate diverse processes such as axon pruning and repulsion, dendritic attraction and branching, regulation of cell migration, vascular remodeling, and growth cone collapse. Both upregulation and downregulation of Plexin A4 has been observed following neural injury suggesting a dynamic role for Sema3A and Plexin A4 in neural maintenance and regeneration. Additionally, Sema3A and therefore its receptor, Plexin A4, have been implicated as possible components of fast-fatigable muscle fiber denervation in ALS.

# Structure
Plexin A4 has ~1890 amino acids that include a likely signal sequence, transmembrane domain, and 12 extracellular N-linked glycosylation sites. It also contains domains consistent with other class A plexins including a Sema domain, three "Met-related sequences"/cysteine clusters, three extracellular glycine-proline repeats, intracellular SP domains, and a putative intracellular tyrosine kinase phosphorylation site.

# Tissue distribution
In the adult rat central nervous system (CNS), plexin A4 was present in neurons and fibers throughout the brain and spinal cord, including neocortex, hippocampus, lateral hypothalamus, red nucleus, facial nucleus, and the mesencephalic trigeminal nucleus. Fibers expressed Plexin A4 in the lateral septum, nucleus accumbens, several thalamic nuclei, substantia nigra pars reticulata, zona incerta, pontine reticular formation, as well as in several cranial nerve nuclei. Plexin A4 has been found in dorsal and, to a greater extent, ventral horns of the spinal cord. Both motor neurons and interneurons in the ventral horn express Plexin A4. Motor axons exiting via the ventral roots and the ascending and descending white matter tracts express Plexin A4. In dorsal root ganglia, Plexin A4 is expressed in the neuronal cell bodies as well as the central and peripheral processes of those cells.
PPP1R9B
Neurabin-2 is a protein that in humans is encoded by the PPP1R9B gene.
Spinophilin is a regulatory subunit of protein phosphatase-1 catalytic subunit (PP1; see MIM 176875) and is highly enriched in dendritic spines, specialized protrusions from dendritic shafts that receive most of the excitatory input in the central nervous system (Allen et al., 1997).

# Interactions
PPP1R9B has been shown to interact with PPP1CB, PPP1CA, Dopamine receptor D2, P16, PPP1CC, T-cell lymphoma invasion and metastasis-inducing protein 1 and PPP1R2.
PPP2R1A
Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform is an enzyme that in humans is encoded by the PPP2R1A gene. In the plant Arabidopsis thaliana a similar enzyme is encoded by the RCN1 gene (At1g25490).

# Function
This gene encodes a constant regulatory subunit of protein phosphatase 2. Protein phosphatase 2 is one of the four major Ser/Thr phosphatases, and it is implicated in the negative control of cell growth and division. It consists of a common heteromeric core enzyme, which is composed of a catalytic subunit and a constant regulatory subunit, that associates with a variety of regulatory subunits. The constant regulatory subunit A serves as a scaffolding molecule to coordinate the assembly of the catalytic subunit and a variable regulatory B subunit. This gene encodes an alpha isoform of the constant regulatory subunit A.

# Interactions
PPP2R1A has been shown to interact with:
- CTTNBP2NL,
- FAM40A,
- PPP2CB, PPP2CA, PPP4C,
- PPP2R2A,
- PPP2R3B,
- PPP2R5A.
- STK24,
- STRN, and
- STRN3.

# Arabidopsis RCN1
RCN1 At1g25490 is one of three genes in Arabidopsis encoding Phosphoprotein Phosphatase 2A Regulatory Subunit A (PP2Aa). The association of different b subunits with a PP2Aa-PP2ac dimer is believed to determine substrate specificity.
PPP2R3B
Serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta is an enzyme that in humans is encoded by the PPP2R3B gene.

# Function
Protein phosphatase 2 (formerly named type 2A) is one of the four major Ser/Thr phosphatases and is implicated in the negative control of cell growth and division. Protein phosphatase 2 holoenzymes are heterotrimeric proteins composed of a structural subunit A, a catalytic subunit C, and a regulatory subunit B. The regulatory subunit is encoded by a diverse set of genes that have been grouped into the B/PR55, B'/PR61, and B''/PR72 families. These different regulatory subunits confer distinct enzymatic specificities and intracellular localizations to the holozenzyme. The product of this gene belongs to the B'' family. The B'' family has been further divided into subfamilies. The product of this gene belongs to the beta subfamily of regulatory subunit B''. Alternative splicing results in multiple transcript variants encoding different isoforms.

# Interactions
PPP2R3B has been shown to interact with PPP2R1B, PPP2R1A, CDC6 and PPP2CA.
PPP2R5C
Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform is an enzyme that in humans is encoded by the PPP2R5C gene.

# Function
The product of this gene belongs to the Protein phosphatase 2A regulatory subunit B family. Protein phosphatase 2A is one of the four major Ser/Thr phosphatases, and it is implicated in the negative control of cell growth and division. It consists of a common heteromeric core enzyme, which is composed of a catalytic subunit and a constant regulatory subunit, that associates with a variety of regulatory subunits. The B regulatory subunit might modulate substrate selectivity and catalytic activity. This gene encodes a gamma isoform of the regulatory subunit B56 subfamily. Alternatively spliced transcript variants encoding different isoforms have been identified.

# Interactions
PPP2R5C has been shown to interact with PPP2R1B, PPP2CA and PPP2R5A.