From cf2a86ae51e46f6ec1d4b43ef8f6d605532fc00e Mon Sep 17 00:00:00 2001 From: Michel Dumontier Date: Thu, 8 Feb 2018 16:04:42 -0400 Subject: [PATCH] moving files --- ontology/scrap/leontis-westhof-rna.owl | 444 --- ontology/scrap/rna-primitive.owl | 2222 --------------- ontology/scrap/rna.owl | 3482 ------------------------ ontology/scrap/saenger-rna.owl | 710 ----- 4 files changed, 6858 deletions(-) delete mode 100644 ontology/scrap/leontis-westhof-rna.owl delete mode 100644 ontology/scrap/rna-primitive.owl delete mode 100644 ontology/scrap/rna.owl delete mode 100644 ontology/scrap/saenger-rna.owl diff --git a/ontology/scrap/leontis-westhof-rna.owl b/ontology/scrap/leontis-westhof-rna.owl deleted file mode 100644 index 0f6f21fd..00000000 --- a/ontology/scrap/leontis-westhof-rna.owl +++ /dev/null @@ -1,444 +0,0 @@ - - - - - - - - - - - - -]> - - - - - Michel Dumontier - Leontis-Westhof RNA Nomenclature ontology - Jose Cruz-Toledo - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/ontology/scrap/rna-primitive.owl b/ontology/scrap/rna-primitive.owl deleted file mode 100644 index e90a67c3..00000000 --- a/ontology/scrap/rna-primitive.owl +++ /dev/null @@ -1,2222 +0,0 @@ - - - - - - - - - - -]> - - - - - Francois Major - RNA ontology - Jose Cruz-Toledo - Michel Dumontier - - - - - - - - - - - - - - - - - - - - - has disposition - A relation between an entitty and the disposition it realizes - - - - - - - - has function - A relation between an entity and a function - - - - - - - - - - - - - - has quality - A relation between an entity and the quality that inheres in it - - - - - - - - has role - The relation between an entity and a role - - - - - - - - - - - - - AA base pair - - A base pair involving two Adenines - - - - - - - - Adenosine monophosphate - - pubchem:6083 - - - - - - - - AT base pair - - Base pair involving Adenine and Thymine - - - - - - - - Adenosine triphosphate - - pubchem:5957 - - - - - - - - AU base pair - - A base pair involving Adenine and Uracil - - - - - - - - adenine - - pubchem:190 - - - - - - - - adenosine - - pubchem:60961 - - - - - - - - adjacent stacking - - Nucleotide base stacking between adjacent bases. - - - - - - - - - aldohexose - A hexose with an aldehyde functional group in position 1. - - - - - - - - aldopentose - - A pentose with an aldehyde functional group in position 1. - - - - - - - - amino acid - - Molecule containing both an amine and a carboxyl functional group with the general formula H2NCHRCOOH (where R is an organic -substituent) - - - - - - - - anti conformation - - The anti conformation aligns the base away from the ribose. - - - - - - - - antiparallel base pair - - A base pair where the normals are antiparallel. - - - - - - - - aptamer - - nucleic acid or peptide that binds some chemical - - - - - - - - atom orientation in plane role - - - - - - - - - base conformation - - Relative orientation of the nitrogenous base with respect to the ribose. This rotation is about the X bond (glycosidic bond). - - - - - - - - base normal oriented base pair - - A spatial interaction between nucleotides that depends on the direction of their normals. - - - - - - - - base-normal oriented stacking - - Base stacking in which the base normal vector, q, in terms of the pyrimidine ring normal vector, n. In pyrimidines, q is defined as n, the rotational vector obtained from a right-handed roation around the pyrimidine ring from atoms 1 to 6. In purines, q is defined as -n. - - - - - - - - bifurcated face - - - - - - - - - bifurcated hoogsteen face - - Face composed by the following atoms: -Adenine (Nitrogen 6) or Guanine (Oxygen 6), Uracil (Oxygen 4) or Cytosine (Nitrogen 4) - - - - - - - - bifurcated sugar face - - Face composed by the following atoms: -Adenine (Carbon 2) or Guanine (Nitrogen 2), Y (Oxygen 2) -Where Y = Pyrimidines - - - - - - - - biomolecule - - Organic molecule that is produced by a living organism - - - - - - - - c1 prime endo role - - - - - - - - - c1 prime exo role - - - - - - - - - c2 prime endo role - - - - - - - - - c2 prime exo role - - - - - - - - - c3 prime endo role - - - - - - - - - c3 prime exo role - - - - - - - - - c4 prime endo role - - - - - - - - - c4 prime exo role - - - - - - - - - c8 face - - Face composed by the following atom: -R (Carbon 2) -Where R = Purines - - - - - - - - CA base pair - - A base pair involving a Cytosine and an Adenine - - - - - - - - CC base pair - - A base pair involving two Cytosines - - - - - - - - - pubchem:6131 - Cytosine monophosphate - - - - - - - - Cytidine Triphosphate - - pubchem:6176 - - - - - - - - CU base pair - - A base pair involving a Cytosine and a Uracil - - - - - - - - canonical base pair - - A base pair interaction between Adenine and Thymine, Guanine and Cytosine in DNA. In RNA basepairs involving only Thymine and Uracil. - - - - - - - - carbohydrate - - A molecule whose formula can be reduced into (CH20)n, for n >= 3 - - - - - - - - chemical - - Any material with a definite chemical composition. - - - - - - - - cis base pair - - A base pair in which both glycosidic bonds are oriented on the same side of the line that splits the plane evenly in two. - - - - - - - - conformation - - The three-dimensional structure of a molecule. - - - - - - - - cytidine - - pubchem:6175 - - - - - - - - cytosine - - pubchem:597 - - - - - - - - DNA - deoxyribonucleic acid - - A single or double standed linear polymer of nucleotide monophosphates, limited to at least 2 of the following deoxy ribonucleotides: AMP, CMP, GMP or UMP. - - - - - - - - Deoxyribonucleoside - - A nucleoside that has a deoxyribose as its sugar - - - - - - - - deoxyribonucleotide - - A nucleotide that has a deoxyribose as its sugar - - - - - - - - deoxyribose - - pubchem:439576 - - - - - - - - deoxythymidine - - pubchem:5789 - - - - - - - - double stranded nucleic acid - - Two complementary Nucleic Acid strands (of the same type) that exhibit base pairng interactions between them to form helical -structures - - - - - - - - downward stacking - - Downward stacking occurs between bases A and B when the normal of B faces the underside of A, whose normal faces away from B. - - - - - - - - edge interaction - - An interaction between nucleotides based on which edges the hydrogen bonds are formed. - - - - - - - - endo role - - When considering a horizontal plane on the furanose, and teh C5' atom is on the left side, the atoms located over the plane are said to be endo to the C5' - - - - - - - - envelope conformation - - The structural conformation of a furanose when only one of its five atoms (C1', C2', C3', C4' or O4') is out of the plane formed by the remaining four atoms. - - - - - - - - exo role - - When considering a horizontal plane on the furanose, and teh C5' atom is on the left side, the atoms located under the plane are said to be exo to the C5' - - - - - - - - face interaction - - An interaction between nucleotides based on which faces the hydrogen bonds are formed. - - - - - - - - face away role - - - - - - - - - facing towards role - - - - - - - - - furanose - - A five-membered-cyclic carbohydrate - - - - - - - - furanose conformation - - The structural conformation of a furanose. - - - - - - - - GA base pair - - A base pair involving Guanine and Adenine - - - - - - - - GC base pair - - A base pair involving Guanine and Cytosine - - - - - - - - GG base pair - - A base pair involving two Guanines - - - - - - - - Guanosine monophosphate - - pubchem:6804 - - - - - - - - - Guanosine triphosphate - pubchem:6830 - - - - - - - - GU base pair - - A base pair involving Guanine and Uracil - - - - - - - - glucose - - pubchem:5793 - - - - - - - - glycogen - - pubchem:439177 - - - - - - - - glycosyl bond oriented base pair - - A base pair that depends on the glycosyl bond orientation. - - - - - - - - guanine - - pubchem:764 - - - - - - - - guanosine - - - - - - - - pubchem:6802 - - - - - - - - heptose - - A seven-carbon Carbohydrate - - - - - - - - hexose - - A six-carbon carbohydrate - - - - - - - - hoogsteen edge - - Edge composed by the following atoms: -Adenine (Nitrogen 6) or Guanine (Oxygen 6), R (Nitrogen 7), Uracil (Oxygen 4) or Cytosine (Nitrogen 4), Y (Carbon 5), R (Carbon 8) -Where R = Purines and Y = Pyrimidines - - - - - - - - - - - - - - - - Hoogsteen-Hoogsteen base pair - - A base pair involving two hoogsteen edges - - - - - - - - hoogsteen hoogsteen face - - Face composed by the following atoms: -R(Nitrogen 7) , Y (Carbon 5) -Where Y = Pyrimidines and R = Purines - - - - - - - - Hoogsteen-sugar base pair - - A base pair involving a Hoogsteen and a Sugar edge - - - - - - - - hoogsteen watson face - - Face composed by the following atoms: -Adenine (Nitrogen 6) or Guanine (Oxygen 6), Uracil (Oxygen 4) or Cytosine (Nitrogen 4) - - - - - - - - - pubchem:6021 - inosine - - - - - - - - interaction - - - - - - - - - interactor - - A chemical entity that produces a mutual or reciprocal action on itself or another chemical entity - - - - - - - - inward stacking - - Inward stacking occurs between bases A and B when their normals face each other. - - - - - - - - ketohexose - - A hexose with an ketone functional group in position 2. - - - - - - - - ketopentose - - A pentose with an ketone functional group in position 2. - - - - - - - - ligand - - Chemical that binds to a specific site on a biomolecule, and either causes a biochemical change or prevents one from -occuring. - - - - - - - - lipid - - Non polymeric largely hydrophobic biomolecules - - - - - - - - mature-mRNA - - - - - - - - - molecule - - A chemical of definite composition with covalently bonded atoms. - - - - - - - - monosaccharide - - Basic carbohydrate unit - - - - - - - - natural aptamer - - Aptamer that is not generated from an in virto experiment - - - - - - - - nitrogenous base - - Organic compound that acts as a base due to the lone pair of electrons bourne by its nitrogen atom - - - - - - - - non-adjacent stacking - - Nucleotide base stacking between non-adjacent bases. - - - - - - - - non-canonical base pair - - A base pair involving alternate hydrogen bonding patterns. - - - - - - - - nucleic acid - - A polymer composed of nucleotide residues linked in a linear sequence by 3'-5' phosphodiester -linkages. - - - - - - - - nucleic acid aptamer - - An aptamer that is composed from Nucleic Acids - - - - - - - - nucleic acid or component - - Components that comprise Nucleic Acids - - - - - - - - nucleoside - - Purine or pyrimidine base that is attached to a ribose or deoxyribose - - - - - - - - nucleotide - - Purine or pyrimidine base that is attached to a ribose or deoxyribose, (Nucleoside) and is also attached to at least one -phosphate group - - - - - - - - nucleotide base pair - - An interaction involving hydrogen bonds between two nucleotides. - - - - - - - - nucleotide base stacking - - A spatial interaction between nucleotides. - - - - - - - - nucleotide diphosphate - - A nucleotide having 2 phosphates. - - - - - - - - nucleotide edge - - - - - - - - - nucleotide face - - A part of the nucleotide ribose or base, capable of forming hydrogen bonds. - - - - - - - - nucleotide interaction - - An interaction involving at least one nucleotide or any part thereof. - - - - - - - - nucleotide interaction role - - - - - - - - - A nucleotide that is attached to one phosphate - nucleotide monophosphate - - - - - - - - - nucleotide stacking role - - - - - - - - - nucleotide triphosphate - - A nucleotide attached to 3 phosphates. - - - - - - - - o2 prime face - - Face composed by the following atom: -Furanose O2' - - - - - - - - o4 prime endo role - - - - - - - - - o4 prime exo role - - - - - - - - - - - - - - - outward stacking - - Outward stacking occurs between bases A and B when their normals face away from each other. - - - - - - - - parallel base pair - - A base pair where the normals are parallel. - - - - - - - - pentose - - A five-carbon carbohydrate - - - - - - - - peptide - - (Short) amino acid polymer. - - - - - - - - peptide aptamer - - Aptamer composed by aminoacids - - - - - - - - phosphate - - pubchem:1061 - - - - - - - - phosphate component - - Components that comprise Phosphates - - - - - - - - oligonucleotide - - A single chain polymer composed of nucleotides - - - - - - - - polysaccharide - - A monosaccharide polymer joined together by the glycosidic bond - - - - - - - - pre-mRNA - - - - - - - - - - - - - - - protein - - Amino acid polymer that generally has a biologically active three dimensional fold - - - - - - - - protein or component - - Components that comprise Proteins - - - - - - - - - pseudouridine - pubchem:15047 - - - - - - - - purine - - pubchem:1044 - heterocyclic aromatic compound consisting of a pyrimidine ring fused to an imidazole ring - - - - - - - - purine nucleoside - - A nucleoside that has a purine as its base - - - - - - - - pyranose - - A six-membered-cyclic carbohydrate - - - - - - - - pyrimidine - - pubchem:9260 - Six member heterocyclic aromatic compound containing two nitrogen atoms at positions 1 and 3 - - - - - - - - pyrimidine nucleoside - - A nucleoside that has a pyrimidine as its base - - - - - - - - - - - - - - RNA - ribonucleic acid - - A single or double standed linear polymer of nucleotide monophosphates, limited to at least 2 of the following -ribonucleotides: AMP, CMP, GMP or UMP. - - - - - - - - receptor - - Biomolecule that binds some ligand that elicits some response - - - - - - - - relatively oriented base pair - - A base pair that depends on a relative orientation. - - - - - - - - ribonucleoside - - A nucleoside that has a ribose as its sugar - - - - - - - - ribonucleotide - - A nucleotide that has a ribose as its sugar - - - - - - - - ribose - - pubchem:993 - - - - - - - - - - - - - - role player - - A roleplayer is a defined class of entities that must have a relation -to a role as part of the necessary and sufficient conditions. - - - - - - - - single stranded nucleic acid - - A Nucleic Acid strand - - - - - - - - structure determination - - Results of techiniques such as NMR spectroscopy and X-Ray crystallography - - - - - - - - sugar edge - - Edge composed by the following atoms: -Adenine (Carbon 2) or Guanine (Nitrogen 2), R (Nitrogen 3), Y (Oxygen 2), Furanose (Oxygen 2) -Where R = Purines and Y = Pyrimidines - - - - - - - - - - - - - - - - Sugar-Sugar base pair - - A base pair involving two Sugar edges - - - - - - - - sugar sugar face - - Face composed by the following atoms: -R (Nitrogen 3) -Where R = Purines - - - - - - - - sugar watson face - - Face composed by the following atoms: -Guanine (Nitrogen 2), Y (Oxygen 2) -Where Y = Pyrimidines - - - - - - - - syn conformation - - The syn conformation aligns the base towards the ribose. - - - - - - - - synthetic aptamer - - Aptamer that is generated from an in virto experiment - - - - - - - - Thymidine Monophosphate - - pubchem:9700 - - - - - - - - TT base pair - - A base pair involving two Thymines - - - - - - - - tetrose - - A four-carbon carbohydrate - - - - - - - - thymine - - pubchem:1135 - - - - - - - - trans base pair - - A base pair in which both glycosidic bonds are oriented on opposide sides of the line that splits the plane evenly in two. - - - - - - - - triose - - A three-carbon carbohydrate - - - - - - - - twist conformation - - The structural conformation of a furanose when two of its five atoms (C1', C2', C3', C4' or O4') are on opposite sides of the plane formed by the remaining three atoms. - - - - - - - - Uridine Monophosphate - - pubchem:6030 - - - - - - - - Uridine triphosphate - - pubchem:6133 - - - - - - - - UU base pair - - A base pair involving two Uracils - - - - - - - - upward stacking - - Upward stacking occurs between bases A and B when the normal of base A faces the underside of base B, whose normal faces away from A. - - - - - - - - uracil - - pubchem:1174 - - - - - - - - Uridine - - pubchem:6029 - - - - - - - - watson edge - - Edge composed by the following atoms: -Adenine (Nitrogen 6) or Guanine (Oxygen 6), R (Nitrogen 1), Adenine (Carbon 2) or Guanine (Nitrogen 2), Uracil (Oxygen 4) or Cytosine -(Nitrogen 4), Y (Nitrogen 3), Y (Oxygen 2) -Where R = Purines and Y = Pyrimidines - - - - - - - - - - - - - - - - Watson-Hoogsteen base pair - - A base pair involving a Watson and a Hoogsteen edge - - - - - - - - watson hoogsteen face - - Face composed by the following atoms: -Adenine (Nitrogen 6) or Guanine (Oxygen 6), Uracil (Oxygen 4) or Cytosine (Nitrogen 4) - - - - - - - - Watson-Hoogsteen base pair - - A base pair involving a Watson and a Sugar edge - - - - - - - - watson sugar face - - Face composed by the following atoms: -Guanine (Nitrogen 2), Y (Oxygen 2) -Where Y = Pyrimidines - - - - - - - - Watson-Watson base pair - - A base pair involving two Watson edges - - - - - - - - watson watson face - - Face composed by the following atoms: -R (Nitrogen 1), Y (Nitrogen 3) -Where Y = Pyrimidines and R = Purines - - - - - - - - deoxyadenosine monophosphate - - - - - - - - - deoxycytosine monophosphate - - - - - - - - - deoxyguanosine monophosphate - - - - - - - - - double stranded DNA - - Two complementary DNA strands that exhibit base pairng interactions between them to form helical structures - - - - - - - - double stranded RNA - - Two complementary RNA that exhibit base pairng interactions between them to form helical structures - - - - - - - - guide RNA - - - - - - - - - messenger RNA - - Carries information about amino acids sequence to the ribosomes. - - - - - - - - microRNA - - Single stranded RNA molecule which regulates gene expression - - - - - - - - ribosomal RNA - - Catalytic component of ribosomes. - - - - - - - - small cytoplasmic RNA - - - - - - - - - small genomic RNA - - - - - - - - - small hairpin RNA - - - - - - - - - small interfering RNA - - - - - - - - - small nuclear RNA - - Short RNA molecules found in the nuclei of eukaryotic cells. They are involved in a variety of processes such as RNA splicing, regulation of transcription factors or RNA polymerase II activity, and are also involved in the maintence of telomeres. - - - - - - - - small nucleolar RNA - - They guide methylations or pseudouridylations of ribosomal RNAs and other genes. - - - - - - - - single stranded DNA - - A single stranded DNA - - - - - - - - single stranded RNA - - A single stranded RNA - - - - - - - - transfer RNA - - RNA consisting of 74-95 nucleotides that transfers a specific amino acid to a growing polypeptide chain at the ribosomal site of protein synthesis during translation. - - - - - - - - transfer-messenger RNA - - Found in bacteria and plastids. It tags proteins encoded by mRNAs that lack stop codons for degradation and prevents the ribosome from stalling. - - - - - - - diff --git a/ontology/scrap/rna.owl b/ontology/scrap/rna.owl deleted file mode 100644 index 23e45321..00000000 --- a/ontology/scrap/rna.owl +++ /dev/null @@ -1,3482 +0,0 @@ - - - - - - - - - - -]> - - - - - Francois Major - RNA ontology - Michel Dumontier - Jose Cruz-Toledo - - - - - - - - - - - - - - - - - - - - - - - - - - - - has disposition - A relation between an entitty and the disposition it realizes - - - - - - - - has function - A relation between an entity and a function - - - - - - - - - - - - - - - - - - - - has quality - A relation between an entity and the quality that inheres in it - - - - - - - - has role - The relation between an entity and a role - - - - - - - - - - - - - - - - - - - - - - - - - AA base pair - - - - - - - - 2 - - - - - A base pair involving two Adenines - - - - - - - - Adenosine monophosphate - - - - - - 1 - - - - - - - 1 - - - pubchem:6083 - - - - - - - - AT base pair - - - - - - - - 1 - - - - - 1 - - - - - Base pair involving Adenine and Thymine - - - - - - - - Adenosine triphosphate - - - - - - 1 - - - - - - - 3 - - - pubchem:5957 - - - - - - - - AU base pair - - - - - - - - 1 - - - - - 1 - - - - - A base pair involving Adenine and Uracil - - - - - - - - adenine - - pubchem:190 - - - - - - - - adenosine - - - - - - - - - pubchem:60961 - - - - - - - - adjacent stacking - - - Nucleotide base stacking between adjacent bases. - - - - - - - - - aldohexose - A hexose with an aldehyde functional group in position 1. - - - - - - - - aldopentose - - A pentose with an aldehyde functional group in position 1. - - - - - - - - amino acid - - - Molecule containing both an amine and a carboxyl functional group with the general formula H2NCHRCOOH (where R is an organic -substituent) - - - - - - - - anti conformation - - - The anti conformation aligns the base away from the ribose. - - - - - - - - antiparallel base pair - - - A base pair where the normals are antiparallel. - - - - - - - - aptamer - - - - - - - - - - - - - - - - - - - - - - - - - - nucleic acid or peptide that binds some chemical - - - - - - - - atom orientation in plane role - - - - - - - - - - base conformation - - - - - - - - - - - Relative orientation of the nitrogenous base with respect to the ribose. This rotation is about the X bond (glycosidic bond). - - - - - - - - base normal oriented base pair - - - - - - - - - - A spatial interaction between nucleotides that depends on the direction of their normals. - - - - - - - - base-normal oriented stacking - - Base stacking in which the base normal vector, q, in terms of the pyrimidine ring normal vector, n. In pyrimidines, q is defined as n, the rotational vector obtained from a right-handed roation around the pyrimidine ring from atoms 1 to 6. In purines, q is defined as -n. - - - - - - - - bifurcated face - - - - - - - - - bifurcated hoogsteen face - - - - - - - - - - - - - - - Face composed by the following atoms: -Adenine (Nitrogen 6) or Guanine (Oxygen 6), Uracil (Oxygen 4) or Cytosine (Nitrogen 4) - - - - - - - - bifurcated sugar face - - - - - - - - - - - - - - Face composed by the following atoms: -Adenine (Carbon 2) or Guanine (Nitrogen 2), Y (Oxygen 2) -Where Y = Pyrimidines - - - - - - - - biomolecule - - Organic molecule that is produced by a living organism - - - - - - - - c1 prime endo role - - - - - - - - - c1 prime exo role - - - - - - - - - c2 prime endo role - - - - - - - - - c2 prime exo role - - - - - - - - - c3 prime endo role - - - - - - - - - c3 prime exo role - - - - - - - - - c4 prime endo role - - - - - - - - - c4 prime exo role - - - - - - - - - c8 face - - - - - - - - Face composed by the following atom: -R (Carbon 8) -Where R = Purines - - - - - - - - CA base pair - - - - - - - - 1 - - - - - 1 - - - - - A base pair involving a Cytosine and an Adenine - - - - - - - - CC base pair - - - - - - - - 2 - - - - - A base pair involving two Cytosines - - - - - - - - - - - - - 1 - - - - - - - 1 - - - pubchem:6131 - Cytosine monophosphate - - - - - - - - Cytidine Triphosphate - - - - - - 3 - - - - - - - 1 - - - pubchem:6176 - - - - - - - - CU base pair - - - - - - - - 1 - - - - - 1 - - - - - A base pair involving a Cytosine and a Uracil - - - - - - - - canonical base pair - - - - - - - - - - - - A base pair interaction between Adenine and Thymine, Guanine and Cytosine in DNA. In RNA basepairs involving only Thymine and Uracil. - - - - - - - - carbohydrate - - A molecule whose formula can be reduced into (CH20)n, for n >= 3 - - - - - - - - chemical - - Any material with a definite chemical composition. - - - - - - - - cis base pair - - - A base pair in which both glycosidic bonds are oriented on the same side of the line that splits the plane evenly in two. - - - - - - - - conformation - - - - The three-dimensional structure of a molecule. - - - - - - - - cytidine - - - - - - - - pubchem:6175 - - - - - - - - cytosine - - pubchem:597 - - - - - - - - DNA - deoxyribonucleic acid - - - - - - - - - - - - - - - - A single or double standed linear polymer of nucleotide monophosphates, limited to at least 2 of the following deoxy ribonucleotides: AMP, CMP, GMP or UMP. - - - - - - - - Deoxyribonucleoside - - - - - - - - A nucleoside that has a deoxyribose as its sugar - - - - - - - - deoxyribonucleotide - - - - - - - - - A nucleotide that has a deoxyribose as its sugar - - - - - - - - deoxyribose - - - pubchem:439576 - - - - - - - - deoxythymidine - - - - - - - - - - - - - - pubchem:5789 - - - - - - - - double stranded nucleic acid - - - - - - 2 - - - Two complementary Nucleic Acid strands (of the same type) that exhibit base pairng interactions between them to form helical -structures - - - - - - - - downward stacking - - Downward stacking occurs between bases A and B when the normal of B faces the underside of A, whose normal faces away from B. - - - - - - - - edge interaction - - - - - - 2 - - - An interaction between nucleotides based on which edges the hydrogen bonds are formed. - - - - - - - - endo role - - - When considering a horizontal plane on the furanose, and the C5' atom is on the left side, the atoms located over the plane are said to be endo to the C5' - - - - - - - - envelope conformation - - - The structural conformation of a furanose when only one of its five atoms (C1', C2', C3', C4' or O4') is out of the plane formed by the remaining four atoms. - - - - - - - - exo role - - When considering a horizontal plane on the furanose, and teh C5' atom is on the left side, the atoms located under the plane are said to be exo to the C5' - - - - - - - - face interaction - - - - - - 2 - - - An interaction between nucleotides based on which faces the hydrogen bonds are formed. - - - - - - - - face away role - - - - - - - - - - facing towards role - - - - - - - - - furanose - - A five-membered-cyclic carbohydrate - - - - - - - - furanose conformation - - The structural conformation of a furanose. - - - - - - - - GA base pair - - - - - - - - 1 - - - - - 1 - - - - - A base pair involving Guanine and Adenine - - - - - - - - GC base pair - - - - - - - - 1 - - - - - 1 - - - - - A base pair involving Guanine and Cytosine - - - - - - - - GG base pair - - - - - - - - 2 - - - - - A base pair involving two Guanines - - - - - - - - Guanosine monophosphate - - - - - - 1 - - - - - - - 1 - - - pubchem:6804 - - - - - - - - - - - - - 1 - - - - - - - 3 - - - Guanosine triphosphate - pubchem:6830 - - - - - - - - GU base pair - - - - - - - - 1 - - - - - 1 - - - - - A base pair involving Guanine and Uracil - - - - - - - - glucose - - pubchem:5793 - - - - - - - - glycogen - - pubchem:439177 - - - - - - - - glycosyl bond oriented base pair - - - - - - - - - - A base pair that depends on the glycosyl bond orientation. - - - - - - - - guanine - - pubchem:764 - - - - - - - - guanosine - - - - - - - - pubchem:6802 - - - - - - - - heptose - - A seven-carbon Carbohydrate - - - - - - - - hexose - - A six-carbon carbohydrate - - - - - - - - hoogsteen edge - - - - - - 1 - - - - - - - 1 - - - - - - - 1 - - - - - - - 1 - - - Edge composed by the following atoms: -Adenine (Nitrogen 6) or Guanine (Oxygen 6), R (Nitrogen 7), Uracil (Oxygen 4) or Cytosine (Nitrogen 4), Y (Carbon 5), R (Carbon 8) -Where R = Purines and Y = Pyrimidines - - - - - - - - - - - - - - - - - - - - - - - - - - Hoogsteen-Hoogsteen base pair - - - - - - - - A base pair involving two hoogsteen edges - - - - - - - - hoogsteen hoogsteen face - - - - - - - - Face composed by the following atoms: -R(Nitrogen 7) , Y (Carbon 5) -Where Y = Pyrimidines and R = Purines - - - - - - - - Hoogsteen-sugar base pair - - - - - - - - - - - - - - - - A base pair involving a Hoogsteen and a Sugar edge - - - - - - - - hoogsteen watson face - - - - - - - - Face composed by the following atoms: -Adenine (Nitrogen 6) or Guanine (Oxygen 6), Uracil (Oxygen 4) or Cytosine (Nitrogen 4) - - - - - - - - - pubchem:6021 - inosine - - - - - - - - interaction - - - - - - - - - - - - - - - - interactor - - - - - - - - A chemical entity that produces a mutual or reciprocal action on itself or another chemical entity - - - - - - - - inward stacking - - Inward stacking occurs between bases A and B when their normals face each other. - - - - - - - - ketohexose - - A hexose with an ketone functional group in position 2. - - - - - - - - ketopentose - - A pentose with an ketone functional group in position 2. - - - - - - - - ligand - - Chemical that binds to a specific site on a biomolecule, and either causes a biochemical change or prevents one from -occuring. - - - - - - - - lipid - - Non polymeric largely hydrophobic biomolecules - - - - - - - - mature-mRNA - - - - - - - - - molecule - - A chemical of definite composition with covalently bonded atoms. - - - - - - - - monosaccharide - - - Basic carbohydrate unit - - - - - - - - natural aptamer - - - Aptamer that is not generated from an in virto experiment - - - - - - - - nitrogenous base - - Organic compound that acts as a base due to the lone pair of electrons bourne by its nitrogen atom - - - - - - - - non-adjacent stacking - - Nucleotide base stacking between non-adjacent bases. - - - - - - - - non-canonical base pair - - - - - - - - - - - - - - - - - A base pair involving alternate hydrogen bonding patterns. - - - - - - - - nucleic acid - - - - - - - - - - - - - A polymer composed of nucleotide residues linked in a linear sequence by 3'-5' phosphodiester -linkages. - - - - - - - - nucleic acid aptamer - - - - - - - - - - - An aptamer that is composed from Nucleic Acids - - - - - - - - nucleic acid or component - - Components that comprise Nucleic Acids - - - - - - - - nucleoside - - - - - - - - - - - - - - - - Purine or pyrimidine base that is attached to a ribose or deoxyribose - - - - - - - - nucleotide - - - - - - - - - - - - - - - - Purine or pyrimidine base that is attached to a ribose or deoxyribose, (Nucleoside) and is also attached to at least one -phosphate group - - - - - - - - nucleotide base pair - - - - - - 2 - - - - An interaction involving hydrogen bonds between two nucleotides. - - - - - - - - nucleotide base stacking - - - - - - - - - - A spatial interaction between nucleotides. - - - - - - - - nucleotide diphosphate - - - - - - - - 2 - - - - - - A nucleotide having 2 phosphates. - - - - - - - - nucleotide edge - - - - - - - - - - - - - - - - - - - nucleotide face - - A part of the nucleotide ribose or base, capable of forming hydrogen bonds. - - - - - - - - nucleotide interaction - - - - - - - - An interaction involving at least one nucleotide or any part thereof. - - - - - - - - nucleotide interaction role - - - - - - - - - A nucleotide that is attached to one phosphate - nucleotide monophosphate - - - - - - - - 1 - - - - - - - - - - 1 - - - - - - - - - - nucleotide stacking role - - - - - - - - - nucleotide triphosphate - - - - - - - - 3 - - - - - - A nucleotide attached to 3 phosphates. - - - - - - - - o2 prime face - - Face composed by the following atom: -Furanose O2' - - - - - - - - o4 prime endo role - - - - - - - - - o4 prime exo role - - - - - - - - - - - - - - - outward stacking - - Outward stacking occurs between bases A and B when their normals face away from each other. - - - - - - - - parallel base pair - - A base pair where the normals are parallel. - - - - - - - - pentose - - A five-carbon carbohydrate - - - - - - - - peptide - - (Short) amino acid polymer. - - - - - - - - peptide aptamer - - - Aptamer composed by aminoacids - - - - - - - - phosphate - - pubchem:1061 - - - - - - - - phosphate component - - Components that comprise Phosphates - - - - - - - - oligonucleotide - - - - - - - - - - - - - - - - 2 - - - A single chain polymer composed of nucleotides - - - - - - - - polysaccharide - - - - - - 2 - - - A monosaccharide polymer joined together by the glycosidic bond - - - - - - - - pre-mRNA - - - - - - - - - - - - - - - protein - - - - - - - - - - - - - Amino acid polymer that generally has a biologically active three dimensional fold - - - - - - - - protein or component - - Components that comprise Proteins - - - - - - - - - pseudouridine - pubchem:15047 - - - - - - - - purine - - - pubchem:1044 - heterocyclic aromatic compound consisting of a pyrimidine ring fused to an imidazole ring - - - - - - - - purine nucleoside - - - - - - - - A nucleoside that has a purine as its base - - - - - - - - pyranose - - A six-membered-cyclic carbohydrate - - - - - - - - pyrimidine - - pubchem:9260 - Six member heterocyclic aromatic compound containing two nitrogen atoms at positions 1 and 3 - - - - - - - - pyrimidine nucleoside - - - - - - - - A nucleoside that has a pyrimidine as its base - - - - - - - - - - - - - - RNA - ribonucleic acid - - - - - - - - - - - - - - - A single or double standed linear polymer of nucleotide monophosphates, limited to at least 2 of the following -ribonucleotides: AMP, CMP, GMP or UMP. - - - - - - - - receptor - - Biomolecule that binds some ligand that elicits some response - - - - - - - - relatively oriented base pair - - A base pair that depends on a relative orientation. - - - - - - - - ribonucleoside - - - - - - - - A nucleoside that has a ribose as its sugar - - - - - - - - ribonucleotide - - - - - - 1 - - - A nucleotide that has a ribose as its sugar - - - - - - - - ribose - - pubchem:993 - - - - - - - - - - - - - - role player - - - - - - - - - - - - - - A roleplayer is a defined class of entities that must have a relation -to a role as part of the necessary and sufficient conditions. - - - - - - - - single stranded nucleic acid - - A Nucleic Acid strand - - - - - - - - structure determination - - Results of techiniques such as NMR spectroscopy and X-Ray crystallography - - - - - - - - sugar edge - - - - - - 1 - - - - - - - 1 - - - - - - - 1 - - - Edge composed by the following atoms: -Adenine (Carbon 2) or Guanine (Nitrogen 2), R (Nitrogen 3), Y (Oxygen 2), Furanose (Oxygen 2) -Where R = Purines and Y = Pyrimidines - - - - - - - - - - - - - - - - - - - - - - - - - Sugar-Sugar base pair - - - - - - - - A base pair involving two Sugar edges - - - - - - - - sugar sugar face - - - - - - - - Face composed by the following atoms: -R (Nitrogen 3) -Where R = Purines - - - - - - - - sugar watson face - - - - - - - - Face composed by the following atoms: -Guanine (Nitrogen 2), Y (Oxygen 2) -Where Y = Pyrimidines - - - - - - - - syn conformation - - The syn conformation aligns the base towards the ribose. - - - - - - - - synthetic aptamer - - Aptamer that is generated from an in virto experiment - - - - - - - - Thymidine Monophosphate - - - - - - 1 - - - - - - - 1 - - - pubchem:9700 - - - - - - - - TT base pair - - - - - - - - 2 - - - - - A base pair involving two Thymines - - - - - - - - tetrose - - A four-carbon carbohydrate - - - - - - - - thymine - - pubchem:1135 - - - - - - - - trans base pair - - A base pair in which both glycosidic bonds are oriented on opposide sides of the line that splits the plane evenly in two. - - - - - - - - triose - - A three-carbon carbohydrate - - - - - - - - twist conformation - - The structural conformation of a furanose when two of its five atoms (C1', C2', C3', C4' or O4') are on opposite sides of the plane formed by the remaining three atoms. - - - - - - - - Uridine Monophosphate - - - - - - 1 - - - - - - - 1 - - - pubchem:6030 - - - - - - - - Uridine triphosphate - - - - - - 1 - - - - - - - 3 - - - pubchem:6133 - - - - - - - - UU base pair - - - - - - - - 2 - - - - - A base pair involving two Uracils - - - - - - - - upward stacking - - Upward stacking occurs between bases A and B when the normal of base A faces the underside of base B, whose normal faces away from A. - - - - - - - - uracil - - pubchem:1174 - - - - - - - - Uridine - - - - - - - - pubchem:6029 - - - - - - - - watson edge - - - - - - 1 - - - - - - - 1 - - - - - - - 1 - - - - - - - 1 - - - - - - - 1 - - - Edge composed by the following atoms: -Adenine (Nitrogen 6) or Guanine (Oxygen 6), R (Nitrogen 1), Adenine (Carbon 2) or Guanine (Nitrogen 2), Uracil (Oxygen 4) or Cytosine -(Nitrogen 4), Y (Nitrogen 3), Y (Oxygen 2) -Where R = Purines and Y = Pyrimidines - - - - - - - - - - - - - - - - - - - - - - - - - Watson-Hoogsteen base pair - - - - - - - - - - - - - - - - A base pair involving a Watson and a Hoogsteen edge - - - - - - - - watson hoogsteen face - - - - - - - - Face composed by the following atoms: -Adenine (Nitrogen 6) or Guanine (Oxygen 6), Uracil (Oxygen 4) or Cytosine (Nitrogen 4) - - - - - - - - Watson-Hoogsteen base pair - - - - - - - - - - - - - - - - A base pair involving a Watson and a Sugar edge - - - - - - - - watson sugar face - - - - - - - - Face composed by the following atoms: -Guanine (Nitrogen 2), Y (Oxygen 2) -Where Y = Pyrimidines - - - - - - - - Watson-Watson base pair - - - - - - - - A base pair involving two Watson edges - - - - - - - - watson watson face - - - - - - - - Face composed by the following atoms: -R (Nitrogen 1), Y (Nitrogen 3) -Where Y = Pyrimidines and R = Purines - - - - - - - - deoxyadenosine monophosphate - - - - - - 1 - - - - - - - - - - deoxycytosine monophosphate - - - - - - 1 - - - - - - - 1 - - - - - - - - - - deoxyguanosine monophosphate - - - - - - 1 - - - - - - - 1 - - - - - - - - - - double stranded DNA - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Two complementary DNA strands that exhibit base pairng interactions between them to form helical structures - - - - - - - - double stranded RNA - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Two complementary RNA that exhibit base pairng interactions between them to form helical structures - - - - - - - - guide RNA - - - - - - - - - messenger RNA - - Carries information about amino acids sequence to the ribosomes. - - - - - - - - microRNA - - Single stranded RNA molecule which regulates gene expression - - - - - - - - ribosomal RNA - - Catalytic component of ribosomes. - - - - - - - - small cytoplasmic RNA - - - - - - - - - small genomic RNA - - - - - - - - - small hairpin RNA - - - - - - - - - small interfering RNA - - - - - - - - - small nuclear RNA - - Short RNA molecules found in the nuclei of eukaryotic cells. They are involved in a variety of processes such as RNA splicing, regulation of transcription factors or RNA polymerase II activity, and are also involved in the maintence of telomeres. - - - - - - - - small nucleolar RNA - - They guide methylations or pseudouridylations of ribosomal RNAs and other genes. - - - - - - - - single stranded DNA - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A single stranded DNA - - - - - - - - single stranded RNA - - - - - - - - - - - - - - - - - - - - - - - - - - A single stranded RNA - - - - - - - - transfer RNA - - RNA consisting of 74-95 nucleotides that transfers a specific amino acid to a growing polypeptide chain at the ribosomal site of protein synthesis during translation. - - - - - - - - transfer-messenger RNA - - Found in bacteria and plastids. It tags proteins encoded by mRNAs that lack stop codons for degradation and prevents the ribosome from stalling. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/ontology/scrap/saenger-rna.owl b/ontology/scrap/saenger-rna.owl deleted file mode 100644 index 218ba3f5..00000000 --- a/ontology/scrap/saenger-rna.owl +++ /dev/null @@ -1,710 +0,0 @@ - - - - - - - - - - - -]> - - - - - Jose Cruz-Toledo - Michel Dumontier - Saenger RNA Nomenclature ontology - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -