Alignment with ODM2 speciation
ODM2 publishes a set of controlled vocabularies at http://vocabulary.odm2.org/. Its speciation vocabulary names the chemical form in which a measured result is expressed, for example nitrogen reported as nitrate or as ammonium. This page records how each of its concepts is represented in BERVO. It is the first step on issue #66.
Source
The SKOS export at
http://vocabulary.odm2.org/api/v1/speciation/?format=skos, fetched on
2026-09-17. It holds 145 concepts and the scheme itself. Every concept's
definition takes the form "Expressed as X"; that definition is copied into the
BERVO term's Comment.
How the alignment is recorded
- Each ODM2 concept becomes a
DbXrefsentry in the formODM2:speciation/<id>, on either an existing BERVO concept or a new one. TheODM2prefix expands tohttp://vocabulary.odm2.org/, so the emitted IRI is the concept's own URI and the same prefix serves the other ODM2 vocabularies later. - The ODM2 identifier (usually a chemical formula) is kept as an exact
synonym, and the ODM2 definition is quoted in the term's
Comment. - Where a CHEBI term for the substance exists and was verified against OLS, it is added as a second cross-reference. Existing BERVO element and ion terms that lacked one gain it at the same time.
- Chemical species sit under Chemical (
BERVO:8000586): elements under Element, ions under Ion, and organic species under a new Organic compound with four subgroups (Polycyclic aromatic hydrocarbon, Alkane, Organohalogen compound, Phthalate ester). Isotopes sit under Isotope, and the two non-chemical concepts under Physical property.
ODM2 concepts mapped to existing BERVO terms
| ODM2 concept | BERVO term | CHEBI added |
|---|---|---|
Al |
Aluminum (BERVO:8000180) |
|
C |
Carbon (BERVO:8000075) |
|
Ca |
Calcium (BERVO:8000108) |
CHEBI:22984 |
Fe |
Iron (BERVO:8000182) |
|
K |
Potassium (BERVO:8000198) |
|
Mg |
Magnesium (BERVO:8000207) |
CHEBI:25107 |
N |
Nitrogen (BERVO:8000167) |
CHEBI:25555 |
Na |
Sodium (BERVO:8000143) |
CHEBI:26708 |
P |
Phosphorus (BERVO:8000001) |
CHEBI:28659 |
O2 |
Oxygen (BERVO:8000124) |
|
NH4 |
Ammonium (BERVO:8000113) |
CHEBI:28938 |
CO3 |
Carbonate (BERVO:8000098) |
CHEBI:41609 |
HCO3 |
Bicarbonate (BERVO:8000141) |
|
NO3 |
Nitrate (BERVO:8000168) |
|
PO4 |
Phosphate (BERVO:8000138) |
CHEBI:18367 |
SO4 |
Sulfate (BERVO:8000228) |
|
CO2 |
Carbon dioxide (BERVO:8000188) |
CHEBI:16526 |
CaCO3 |
Calcium carbonate (BERVO:8000094) |
|
CH4 |
Methane (BERVO:8000024) |
|
H2O |
Water (BERVO:8000102) |
|
EC |
Electrical conductivity (BERVO:8000885) |
|
pH |
pH (BERVO:8000261) |
Two of the 145 concepts are not mapped: Not Applicable and Unknown are
placeholders of the vocabulary rather than speciations. The SKOS export also
describes the scheme itself, which is not a concept.
Points to note
- ODM2
Clis defined as "expressed as chlorine", so it maps to the new element Chlorine, not to Chloride (BERVO:8000036). Chloride's exact synonymClbecomesCl-, withClkept as a related synonym, so that no exact synonym names two terms. - ODM2
NO2is nitrite. It maps to the new Nitrite, not to Nitrogen dioxide (BERVO:8000123), whose synonym is alsoNO2. - ODM2
SiO2is defined as "expressed as silicate". The BERVO term is Silicon dioxide, withsilicaas a synonym, and the comment carries the ODM2 wording. - ODM2
O2maps to Oxygen (BERVO:8000124), which sits under Element withO2as a synonym. No CHEBI cross-reference is added there, because the term is used for dioxygen and the parent says element. - Twelve ODM2 concepts are molecular formulas that stand for several isomers ("C16H10, e.g., fluoranthene, pyrene"). Six of them get a formula-based label such as C16H10 aromatic hydrocarbons, with the named isomers as related synonyms and no CHEBI cross-reference. The rest, such as dichloroethane, trichloroethane, dichlorobenzene, and the methylated naphthalenes, get the generic name, and a CHEBI class cross-reference only where CHEBI has the generic class.
- The cross-reference local part is the slug from the SKOS
rdf:about, which differs from the displayed label where the label has spaces or parentheses:delta2Hfor "delta 2H",C10H6_CH3_2for "C10H6(CH3)2". Each emitted IRI was checked on 2026-09-17 and redirects (301) to the same path with a trailing slash, which returns the concept page. - ODM2 defines
CH3Hgas "Expressed at methylmercury". The typo is verbatim in the export and is quoted as is. - The n-alkane series runs C15 to C29 and then C31. ODM2 has no C30 concept.
- C12H10 aromatic hydrocarbons sits under Organic compound rather than Polycyclic aromatic hydrocarbon, because biphenyl's rings are not fused.
- Methane (
BERVO:8000024) moves under the new Alkane, beside Ethane. - Total alkalinity has no CHEBI term. It sits under Physical property beside pH.
- Aluminum (
BERVO:8000180) already carriesCHEBI:33620, which is "aluminium molecular entity" rather than the atom. It is left as it was.
New terms
| BERVO term | Parent | ODM2 concept | CHEBI |
|---|---|---|---|
Organic compound (BERVO:8000590) |
Chemical | CHEBI:50860 |
|
Polycyclic aromatic hydrocarbon (BERVO:8000591) |
Organic compound | CHEBI:33848 |
|
Alkane (BERVO:8000592) |
Organic compound | CHEBI:18310 |
|
Organohalogen compound (BERVO:8000593) |
Organic compound | CHEBI:17792 |
|
Phthalate ester (BERVO:8000594) |
Organic compound | CHEBI:35484 |
|
Silver (BERVO:8000595) |
Element | Ag |
CHEBI:30512 |
Arsenic (BERVO:8000596) |
Element | As |
CHEBI:27563 |
Boron (BERVO:8000597) |
Element | B |
CHEBI:27560 |
Barium (BERVO:8000598) |
Element | Ba |
CHEBI:32594 |
Beryllium (BERVO:8000599) |
Element | Be |
CHEBI:30501 |
Bromine (BERVO:8000600) |
Element | Br |
CHEBI:22927 |
Cadmium (BERVO:8000601) |
Element | Cd |
CHEBI:22977 |
Chlorine (BERVO:8000602) |
Element | Cl |
CHEBI:23116 |
Cobalt (BERVO:8000603) |
Element | Co |
CHEBI:27638 |
Chromium (BERVO:8000604) |
Element | Cr |
CHEBI:28073 |
Copper (BERVO:8000605) |
Element | Cu |
CHEBI:28694 |
Fluorine (BERVO:8000606) |
Element | F |
CHEBI:24061 |
Mercury (BERVO:8000607) |
Element | Hg |
CHEBI:25195 |
Manganese (BERVO:8000608) |
Element | Mn |
CHEBI:18291 |
Molybdenum (BERVO:8000609) |
Element | Mo |
CHEBI:28685 |
Nickel (BERVO:8000610) |
Element | Ni |
CHEBI:28112 |
Lead (BERVO:8000611) |
Element | Pb |
CHEBI:25016 |
Radium (BERVO:8000612) |
Element | Ra |
CHEBI:33325 |
Rhenium (BERVO:8000613) |
Element | Re |
CHEBI:49882 |
Sulfur (BERVO:8000614) |
Element | S |
CHEBI:26833 |
Antimony (BERVO:8000615) |
Element | Sb |
CHEBI:30513 |
Selenium (BERVO:8000616) |
Element | Se |
CHEBI:27568 |
Silicon (BERVO:8000617) |
Element | Si |
CHEBI:27573 |
Tin (BERVO:8000618) |
Element | Sn |
CHEBI:27007 |
Strontium (BERVO:8000619) |
Element | Sr |
CHEBI:33324 |
Thorium (BERVO:8000620) |
Element | Th |
CHEBI:33385 |
Titanium (BERVO:8000621) |
Element | Ti |
CHEBI:33341 |
Thallium (BERVO:8000622) |
Element | Tl |
CHEBI:30440 |
Uranium (BERVO:8000623) |
Element | U |
CHEBI:27214 |
Vanadium (BERVO:8000624) |
Element | V |
CHEBI:27698 |
Zinc (BERVO:8000625) |
Element | Zn |
CHEBI:27363 |
Zirconium (BERVO:8000626) |
Element | Zr |
CHEBI:33342 |
Nitrite (BERVO:8000627) |
Ion | NO2 |
CHEBI:16301 |
Cyanide (BERVO:8000628) |
Ion | CN- |
CHEBI:17514 |
Methylmercury (BERVO:8000629) |
Ion | CH3Hg |
CHEBI:49747 |
Silicon dioxide (BERVO:8000630) |
Chemical | SiO2 |
CHEBI:30563 |
Deuterium (BERVO:8000631) |
Isotope | delta 2H |
CHEBI:29237 |
Nitrogen-15 (BERVO:8000632) |
Isotope | delta N15 |
CHEBI:36934 |
Oxygen-18 (BERVO:8000633) |
Isotope | delta O18 |
CHEBI:33815 |
Total alkalinity (BERVO:8000634) |
Physical property | TA |
|
Naphthalene (BERVO:8000635) |
Polycyclic aromatic hydrocarbon | C10H8 |
CHEBI:16482 |
Methylnaphthalene (BERVO:8000636) |
Polycyclic aromatic hydrocarbon | C10H7CH3 |
CHEBI:50715 |
Dimethylnaphthalene (BERVO:8000637) |
Polycyclic aromatic hydrocarbon | C10H6(CH3)2 |
CHEBI:48853 |
Trimethylnaphthalene (BERVO:8000638) |
Polycyclic aromatic hydrocarbon | C10H5(CH3)3 |
|
Tetramethylnaphthalene (BERVO:8000639) |
Polycyclic aromatic hydrocarbon | C10H4(CH3)4 |
|
Ethylnaphthalene (BERVO:8000640) |
Polycyclic aromatic hydrocarbon | C10H7C2H5 |
|
Acenaphthylene (BERVO:8000641) |
Polycyclic aromatic hydrocarbon | C12H8 |
CHEBI:33081 |
C12H10 aromatic hydrocarbons (BERVO:8000642) |
Organic compound | C12H10 |
|
Fluorene (BERVO:8000643) |
Polycyclic aromatic hydrocarbon | C13H10 |
CHEBI:28266 |
Methylfluorene (BERVO:8000644) |
Polycyclic aromatic hydrocarbon | C14H12 |
|
Phenanthrene (BERVO:8000645) |
Polycyclic aromatic hydrocarbon | C14H10 |
CHEBI:28851 |
C15H12 aromatic hydrocarbons (BERVO:8000646) |
Polycyclic aromatic hydrocarbon | C15H12 |
|
C16H10 aromatic hydrocarbons (BERVO:8000647) |
Polycyclic aromatic hydrocarbon | C16H10 |
|
Dimethylphenanthrene (BERVO:8000648) |
Polycyclic aromatic hydrocarbon | C16H14 |
|
C17H12 aromatic hydrocarbons (BERVO:8000649) |
Polycyclic aromatic hydrocarbon | C17H12 |
|
C18H12 aromatic hydrocarbons (BERVO:8000650) |
Polycyclic aromatic hydrocarbon | C18H12 |
|
Retene (BERVO:8000651) |
Polycyclic aromatic hydrocarbon | C18H18 |
|
Methylchrysene (BERVO:8000652) |
Polycyclic aromatic hydrocarbon | C19H14 |
|
C20H12 aromatic hydrocarbons (BERVO:8000653) |
Polycyclic aromatic hydrocarbon | C20H12 |
|
Dibenz[a,h]anthracene (BERVO:8000654) |
Polycyclic aromatic hydrocarbon | C22H14 |
CHEBI:35299 |
Dibenzofuran (BERVO:8000655) |
Organic compound | C12H8O |
CHEBI:28145 |
Dibenzothiophene (BERVO:8000656) |
Organic compound | C12H8S |
CHEBI:23681 |
Methyldibenzothiophene (BERVO:8000657) |
Organic compound | C13H10S |
|
Carbazole (BERVO:8000658) |
Organic compound | C12H9N |
CHEBI:27543 |
Benzene (BERVO:8000659) |
Organic compound | C6H6 |
CHEBI:16716 |
Toluene (BERVO:8000660) |
Organic compound | C7H8 |
CHEBI:17578 |
Ethylbenzene (BERVO:8000661) |
Organic compound | C8H10 |
CHEBI:16101 |
Xylene (BERVO:8000662) |
Organic compound | C6H4(CH3)2 |
CHEBI:27338 |
Styrene (BERVO:8000663) |
Organic compound | C8H8 |
CHEBI:27452 |
Phenol (BERVO:8000664) |
Organic compound | C6H5OH |
CHEBI:15882 |
Aniline (BERVO:8000665) |
Organic compound | C6H5NH2 |
CHEBI:17296 |
Nitrobenzene (BERVO:8000666) |
Organic compound | C6H5NO2 |
CHEBI:27798 |
Dinitrophenol (BERVO:8000667) |
Organic compound | C6H4N2O5 |
CHEBI:39352 |
Dinitrotoluene (BERVO:8000668) |
Organic compound | C7H6N2O4 |
CHEBI:23822 |
Isophorone (BERVO:8000669) |
Organic compound | C9H14O |
CHEBI:34800 |
Acetone (BERVO:8000670) |
Organic compound | C3H6O |
CHEBI:15347 |
Butanone (BERVO:8000671) |
Organic compound | C4H8O |
CHEBI:28398 |
Ethylene glycol (BERVO:8000672) |
Organic compound | C2H6O2 |
CHEBI:30742 |
Diethyl phthalate (BERVO:8000673) |
Phthalate ester | C12H14O4 |
CHEBI:34698 |
Benzyl butyl phthalate (BERVO:8000674) |
Phthalate ester | C19H20O4 |
|
Dimethyl terephthalate (BERVO:8000675) |
Organic compound | C10H10O4 |
CHEBI:156286 |
Ethane (BERVO:8000676) |
Alkane | C2H6 |
CHEBI:42266 |
Pentadecane (BERVO:8000677) |
Alkane | C15H32 |
CHEBI:28897 |
Hexadecane (BERVO:8000678) |
Alkane | C16H34 |
CHEBI:45296 |
Heptadecane (BERVO:8000679) |
Alkane | C17H36 |
CHEBI:16148 |
Octadecane (BERVO:8000680) |
Alkane | C18H38 |
CHEBI:32926 |
Nonadecane (BERVO:8000681) |
Alkane | C19H40 |
CHEBI:32927 |
Icosane (BERVO:8000682) |
Alkane | C20H42 |
CHEBI:43619 |
Henicosane (BERVO:8000683) |
Alkane | C21H44 |
CHEBI:32931 |
Docosane (BERVO:8000684) |
Alkane | C22H46 |
CHEBI:46050 |
Tricosane (BERVO:8000685) |
Alkane | C23H48 |
CHEBI:32934 |
Tetracosane (BERVO:8000686) |
Alkane | C24H50 |
CHEBI:32936 |
Pentacosane (BERVO:8000687) |
Alkane | C25H52 |
CHEBI:32938 |
Hexacosane (BERVO:8000688) |
Alkane | C26H54 |
CHEBI:32940 |
Heptacosane (BERVO:8000689) |
Alkane | C27H56 |
CHEBI:32941 |
Octacosane (BERVO:8000690) |
Alkane | C28H58 |
CHEBI:32943 |
Nonacosane (BERVO:8000691) |
Alkane | C29H60 |
CHEBI:7613 |
Hentriacontane (BERVO:8000692) |
Alkane | C31H64 |
CHEBI:5659 |
Chloromethane (BERVO:8000693) |
Organohalogen compound | CH3Cl |
CHEBI:36014 |
Dichloromethane (BERVO:8000694) |
Organohalogen compound | CH2Cl2 |
CHEBI:15767 |
Chloroform (BERVO:8000695) |
Organohalogen compound | CHCl3 |
CHEBI:35255 |
Bromomethane (BERVO:8000696) |
Organohalogen compound | CH3Br |
CHEBI:39275 |
Bromoform (BERVO:8000697) |
Organohalogen compound | CHBr3 |
CHEBI:38682 |
Bromodichloromethane (BERVO:8000698) |
Organohalogen compound | CHBrCl2 |
CHEBI:34591 |
Dibromochloromethane (BERVO:8000699) |
Organohalogen compound | CHBr2Cl |
CHEBI:34627 |
Chloroethane (BERVO:8000700) |
Organohalogen compound | C2H5Cl |
CHEBI:47554 |
Dichloroethane (BERVO:8000701) |
Organohalogen compound | C2H4Cl2 |
|
Trichloroethane (BERVO:8000702) |
Organohalogen compound | C2H3Cl3 |
|
Tetrachloroethane (BERVO:8000703) |
Organohalogen compound | C2H2Cl4 |
|
Hexachloroethane (BERVO:8000704) |
Organohalogen compound | C2Cl6 |
CHEBI:39227 |
Chloroethene (BERVO:8000705) |
Organohalogen compound | C2H3Cl |
CHEBI:28509 |
Trichloroethene (BERVO:8000706) |
Organohalogen compound | C2HCl3 |
CHEBI:16602 |
Tetrachloroethene (BERVO:8000707) |
Organohalogen compound | C2Cl4 |
CHEBI:17300 |
Hexachlorobutadiene (BERVO:8000708) |
Organohalogen compound | C4Cl6 |
CHEBI:5691 |
Hexachlorocyclopentadiene (BERVO:8000709) |
Organohalogen compound | C5Cl6 |
|
Bis(2-chloroethyl) ether (BERVO:8000710) |
Organohalogen compound | C4H8Cl2O |
CHEBI:34573 |
Chlorobenzene (BERVO:8000711) |
Organohalogen compound | C6H5Cl |
CHEBI:28097 |
Dichlorobenzene (BERVO:8000712) |
Organohalogen compound | C6H4Cl2 |
CHEBI:23697 |
Trichlorobenzene (BERVO:8000713) |
Organohalogen compound | C6H3Cl3 |
CHEBI:27096 |
Hexachlorobenzene (BERVO:8000714) |
Organohalogen compound | C6Cl6 |
CHEBI:5692 |
Pentachlorophenol (BERVO:8000715) |
Organohalogen compound | C6HCl5O |
CHEBI:17642 |