ENVO term requests
Habitats that real data is attached to, that a curator has examined, and that no term in ENVO, UBERON, FOODON, BTO or PO fits. These are what HabitatMech is asking the ontology community for.
Each was individually examined against its source path and candidate terms — these are not the bulk-swept remainder. The largest is the single biggest ungrounded concept in the corpus.
| Habitat | Upstream assertions | Sources | Why no term fits |
|---|---|---|---|
| human-associated environment | 52129 | BACDIVE, GOLD | Humans as host, the single largest ungrounded concept at 40432 GOLD organisms. No human-associated environment term exists in ENVO. Deliberately not grounded to animal-associated environment: every host clade would then merge onto one record and the host distinction is the entire content. Highest-value ENVO term request. |
| free-living environment | 19739 | BACDIVE, GOLD | Environmental is BacDive's level-1 counterpart of Host and Engineered. ENVO:01000951 'natural environment' is not its identity or parent: that term requires minimal to no anthropisation, while this provenance bin includes Indoor Air and other settings that do not make that claim. Earlier notes incorrectly cited Paddy, Grove, and herbaceous crop categories as children of BacDive Environmental; the committed MISO research shows they are under Engineered or Host. The near-miss remains an xref so it is not re-derived. |
| mammal-associated environment | 6104 | GOLD | Mammals as host. Parented to animal-associated environment; not grounded there because every host clade would merge onto one record. ENVO term request. |
| endothermic-animal-associated environment | 5130 | MADIN | Category override (#57): a minted identifier gives infer_category nothing to read — no ontology term, no GOLD path — so every Madin habitat named in the BacDive vocabulary fell to OTHER. This is the single largest Madin habitat at 5130 taxa; a warm-blooded animal host is HOST_ASSOCIATED by the same reading as every other host source here. |
| bacterium-associated environment | 3017 | GOLD | GOLD's Host-associated > Microbial > Bacteria: bacteria acting as host for another microbe. No environment term exists for a microbial host; ENVO's organism-associated terms cover plants and animals only. ENVO term request. |
| upper aerodigestive tract environment | 2102 | BACDIVE | Cohort review (subset/disjoint mapping screen): a composite of two sites. UBERON:0001005 'respiratory airway' covers only the airways half and drops the oral cavity, and it is also the correct target for the separate 'Airways' source — adopting it here would merge the two. No single term covers mouth plus airway; the respiratory-tract terms exclude the oral cavity. |
| bird-associated environment | 1848 | GOLD | Birds as host. Parented to animal-associated environment; not grounded there because every host clade would merge onto one record. ENVO term request. |
| insect-associated environment | 1833 | GOLD | Insects as host. Parented to animal-associated environment; not grounded there because every host clade would merge onto one record. ENVO term request. |
| fish-associated environment | 1350 | GOLD | Fish as host. Parented to animal-associated environment; not grounded there because every host clade would merge onto one record. ENVO term request. |
| Rock core/Sediment | 1245 | GOLD | Deep subsurface rock core and sediment sampled together. GOLD conflates two materials in one node, so no single term is honest; parented to sediment as the nearer of the two. |
| ectothermic-animal-associated environment | 999 | MADIN | Category override (#57): a minted identifier gives infer_category nothing to read — no ontology term, no GOLD path — so every Madin habitat named in the BacDive vocabulary fell to OTHER. A cold-blooded animal host is HOST_ASSOCIATED for the same reason as the endotherm one; the thermal distinction is a property of the host, not a different kind of habitat. |
| tree-associated environment | 872 | BACDIVE | A tree as host. No tree-associated environment term exists; BTO:0005516 wood is the material, not the living host. Parented to plant-associated environment as the nearest broader term. ENVO term request. Category set to HOST_ASSOCIATED (#205): the row already parents this to ENVO:01001001 'plant-associated environment', which is the claim that a living plant host defines the habitat, and 17 of the 18 records under that parent are HOST_ASSOCIATED. Same cause as the five domestic-mammal hosts of #200 - the category column was left blank, so the seeder's default stood. The reasoning above is unchanged. |
| mollusc-associated environment | 784 | GOLD | Host-taxon reversal (#114): this was NOT_APPLICABLE on the reasoning that 'a host taxon is not a habitat'. That reasoning is wrong, and the corpus already contradicted it — the same kind of concept was treated as a habitat for Sponge, Nematoda, Reptilia, Mammals, Birds and Fish, which keep their own identity and a term request for an <X>-associated environment. Host-associated > Porifera was NOT_APPLICABLE while its own child Porifera > Sponge was a term request.An organism acting as a host IS a habitat: it is where the microbe lives, and ENVO models exactly this at plant-associated, animal-associated and fungi-associated environment. What is not a habitat is the TAXON TERM — a phylum is a class of organisms, not a place — so the taxon stays an xref (#99) and the concept keeps its own identity as a term-request candidate. NOT_APPLICABLE said the concept is not a habitat, which is a stronger and false claim. |
| invertebrate-associated environment | 621 | GOLD | Invertebrates as host. Parented to animal-associated environment; not grounded there because every host clade would merge onto one record. ENVO term request. |
| bovine-associated environment | 619 | BACDIVE | Host-taxon reversal (#114): this was NOT_APPLICABLE on the reasoning that 'a host taxon is not a habitat'. That reasoning is wrong, and the corpus already contradicted it — the same kind of concept was treated as a habitat for Sponge, Nematoda, Reptilia, Mammals, Birds and Fish, which keep their own identity and a term request for an <X>-associated environment. Host-associated > Porifera was NOT_APPLICABLE while its own child Porifera > Sponge was a term request.An organism acting as a host IS a habitat: it is where the microbe lives, and ENVO models exactly this at plant-associated, animal-associated and fungi-associated environment. What is not a habitat is the TAXON TERM — a phylum is a class of organisms, not a place — so the taxon stays an xref (#99) and the concept keeps its own identity as a term-request candidate. NOT_APPLICABLE said the concept is not a habitat, which is a stronger and false claim. Category set to HOST_ASSOCIATED (#200): the row already claims ENVO:01001002 'animal-associated environment' as the nearest broader term, which is the claim that a living animal host defines the habitat, and every other record carrying that parent is HOST_ASSOCIATED. The category column was left blank here, so the seeder's default stood and five domestic-mammal hosts stayed in OTHER while their siblings did not. The reasoning above is unchanged. |
| crustacean-associated environment | 598 | GOLD | Crustaceans as host. ENVO:01001176 environment associated with an aquatic invertebrate is close but excludes terrestrial crustaceans, so it is not a safe identity either. ENVO term request. |
| Invertebrates-Other | 596 | BACDIVE | Cohort review: NCIT:C17649 'Other' is a bucket with no meaning of its own, and it absorbs 'Rodentia-Other' too — one record labelled 'Other' holding rodents and invertebrates. The invertebrate-associated environment terms in the slice are all aquatic-qualified. Real habitat, no term. |
| myriapod-associated environment | 569 | GOLD | Myriapods as host. Parented to animal-associated environment; not grounded there because every host clade would merge onto one record. ENVO term request. |
| suid-associated environment | 521 | BACDIVE | Host-taxon reversal (#114): this was NOT_APPLICABLE on the reasoning that 'a host taxon is not a habitat'. That reasoning is wrong, and the corpus already contradicted it — the same kind of concept was treated as a habitat for Sponge, Nematoda, Reptilia, Mammals, Birds and Fish, which keep their own identity and a term request for an <X>-associated environment. Host-associated > Porifera was NOT_APPLICABLE while its own child Porifera > Sponge was a term request.An organism acting as a host IS a habitat: it is where the microbe lives, and ENVO models exactly this at plant-associated, animal-associated and fungi-associated environment. What is not a habitat is the TAXON TERM — a phylum is a class of organisms, not a place — so the taxon stays an xref (#99) and the concept keeps its own identity as a term-request candidate. NOT_APPLICABLE said the concept is not a habitat, which is a stronger and false claim. Category set to HOST_ASSOCIATED (#200): the row already claims ENVO:01001002 'animal-associated environment' as the nearest broader term, which is the claim that a living animal host defines the habitat, and every other record carrying that parent is HOST_ASSOCIATED. The category column was left blank here, so the seeder's default stood and five domestic-mammal hosts stayed in OTHER while their siblings did not. The reasoning above is unchanged. |
| sponge-associated environment | 499 | BACDIVE, GOLD | Host-taxon reversal (#114): this was NOT_APPLICABLE on the reasoning that 'a host taxon is not a habitat'. That reasoning is wrong, and the corpus already contradicted it — the same kind of concept was treated as a habitat for Sponge, Nematoda, Reptilia, Mammals, Birds and Fish, which keep their own identity and a term request for an <X>-associated environment. Host-associated > Porifera was NOT_APPLICABLE while its own child Porifera > Sponge was a term request.An organism acting as a host IS a habitat: it is where the microbe lives, and ENVO models exactly this at plant-associated, animal-associated and fungi-associated environment. What is not a habitat is the TAXON TERM — a phylum is a class of organisms, not a place — so the taxon stays an xref (#99) and the concept keeps its own identity as a term-request candidate. NOT_APPLICABLE said the concept is not a habitat, which is a stronger and false claim. |
| alga-associated environment | 482 | GOLD, MADIN | Non-habitat screen (#12): 'Host-associated > Algae' was grounded EXACT to FOODON:03411301 'algae', which FOODON defines as 'an informal term for a large, diverse group of photosynthetic eukaryotic ORGANISMS'. An organism is not a habitat, and because the seeder derives a GOLD child's parent from its path node, that identity also became the parent_habitats entry of 14 records under Host-associated > Algae — publishing 'is-a algae the organism group' as a broader-habitat claim 14 times over. The existing organism-identity screen could not see it: it tests ancestry against NCIT and mesh roots, and FOODON files both the organism and the material under one 'organism material' root, so there is no structural signal to test. The concept itself is real — algae as host — and is the same family as the sponge, nematode and reptile requests, so it becomes a term request with the FOODON term kept as an xref (#99) rather than an identity. |
| Contamination | 474 | BACDIVE | Risky-grounding review (#12): the seeder made ENVO:00002204 'anthropogenic contamination feature' the identity of BacDive's 'Contamination' category — the highest-volume risky grounding at 474 strains. The term asserts two things BacDive does not: that the contamination is anthropogenic, and that the thing is a geographic feature with elevated contaminants in its materials. BacDive's category says only that a strain was isolated as a contaminant, which is as often of a product, a culture or a cleanroom as of a place. These are different concepts rather than a broader and a narrower one, so the term is not a parent either — parent_habitats asserts the parent is BROADER. Kept as an xref (#99), which records that upstream saw a connection without this repo asserting one. |
| microbe-associated environment | 465 | GOLD | GOLD's Host-associated > Microbial: a microorganism as host. Same gap as the Bacteria child; ENVO has no microbial-host environment term. |
| caprine-associated environment | 412 | BACDIVE | Host-taxon reversal (#114): this was NOT_APPLICABLE on the reasoning that 'a host taxon is not a habitat'. That reasoning is wrong, and the corpus already contradicted it — the same kind of concept was treated as a habitat for Sponge, Nematoda, Reptilia, Mammals, Birds and Fish, which keep their own identity and a term request for an <X>-associated environment. Host-associated > Porifera was NOT_APPLICABLE while its own child Porifera > Sponge was a term request.An organism acting as a host IS a habitat: it is where the microbe lives, and ENVO models exactly this at plant-associated, animal-associated and fungi-associated environment. What is not a habitat is the TAXON TERM — a phylum is a class of organisms, not a place — so the taxon stays an xref (#99) and the concept keeps its own identity as a term-request candidate. NOT_APPLICABLE said the concept is not a habitat, which is a stronger and false claim. Category set to HOST_ASSOCIATED (#200): the row already claims ENVO:01001002 'animal-associated environment' as the nearest broader term, which is the claim that a living animal host defines the habitat, and every other record carrying that parent is HOST_ASSOCIATED. The category column was left blank here, so the seeder's default stood and five domestic-mammal hosts stayed in OTHER while their siblings did not. The reasoning above is unchanged. |
| lithic environmental material | 381 | BACDIVE | Generic "Geologic" bin spanning rock, sediment and subsurface. ENVO covers each specifically; nothing covers the bin without misattributing the rest. |
| canid-associated environment | 344 | BACDIVE | Host-taxon reversal (#114) reaching the last members of its own family (#194): this was NOT_APPLICABLE, which asserts the source concept is not a habitat. An organism acting as a host IS a habitat, and the corpus already says so for bovine, caprine, equid, leporid and suid, all minted with ENVO:01001002 'animal-associated environment' as parent and the organism term as an xref. Never curated on the question at all: the NOT_APPLICABLE was the seeder's automatic bacdive_non_habitat_target route firing on an NCBITaxon target, and #114's sweep did not reach this row. The taxon term is not the identity - a family is a class of organisms, not a place - so it stays an xref (#99) and the concept keeps its minted identity with a term request. Category HOST_ASSOCIATED: the host is living. |
| internal tissue environment of an endothermic animal | 341 | MADIN | Category override (#57): a minted identifier gives infer_category nothing to read — no ontology term, no GOLD path — so every Madin habitat named in the BacDive vocabulary fell to OTHER. Inside the tissue of a warm-blooded animal host — more specific than the endotherm source, and host-associated for the same reason. |
| murid-associated environment | 325 | BACDIVE | Host-taxon reversal (#114) reaching the last members of its own family (#194): this was NOT_APPLICABLE, which asserts the source concept is not a habitat. An organism acting as a host IS a habitat, and the corpus already says so for bovine, caprine, equid, leporid and suid, all minted with ENVO:01001002 'animal-associated environment' as parent and the organism term as an xref. Reviewed before, but not on this question: the 2026-08-14 REVIEW row (#43) asked only whether the xref was over-narrow and endorsed the seeder's NOT_APPLICABLE as a side effect. That finding stands and is kept - NCBITaxon:10114 'Rattus' drops the mouse half of the source label - so the requested definition covers mouse and rat while the xref records what upstream actually matched. The taxon term is not the identity - a family is a class of organisms, not a place - so it stays an xref (#99) and the concept keeps its minted identity with a term request. Category HOST_ASSOCIATED: the host is living. |
| nematode-associated environment | 300 | GOLD | Nematodes as host. Parented to animal-associated environment. ENVO term request. |
| equid-associated environment | 269 | BACDIVE | Host-taxon reversal (#114): this was NOT_APPLICABLE on the reasoning that 'a host taxon is not a habitat'. That reasoning is wrong, and the corpus already contradicted it — the same kind of concept was treated as a habitat for Sponge, Nematoda, Reptilia, Mammals, Birds and Fish, which keep their own identity and a term request for an <X>-associated environment. Host-associated > Porifera was NOT_APPLICABLE while its own child Porifera > Sponge was a term request.An organism acting as a host IS a habitat: it is where the microbe lives, and ENVO models exactly this at plant-associated, animal-associated and fungi-associated environment. What is not a habitat is the TAXON TERM — a phylum is a class of organisms, not a place — so the taxon stays an xref (#99) and the concept keeps its own identity as a term-request candidate. NOT_APPLICABLE said the concept is not a habitat, which is a stronger and false claim. Category set to HOST_ASSOCIATED (#200): the row already claims ENVO:01001002 'animal-associated environment' as the nearest broader term, which is the claim that a living animal host defines the habitat, and every other record carrying that parent is HOST_ASSOCIATED. The category column was left blank here, so the seeder's default stood and five domestic-mammal hosts stayed in OTHER while their siblings did not. The reasoning above is unchanged. |
| brown-alga-associated environment | 231 | GOLD | Non-habitat screen (#12): grounded EXACT to FOODON:03412395 'brown algae', which FOODON uses for the TAXON — red algae is defined there as 'one of the oldest groups of eukaryotic algae, and one of the largest phyla' — not for a habitat. An organism group is not a place, and the GOLD path says host-associated, so the concept is the environment the alga provides. Same family as the sponge, nematode and reptile requests. The FOODON term is kept as an xref (#99), which records what the label matched without asserting the record is a phylum. |
| diatom-associated environment | 218 | GOLD | Non-habitat screen review (#108): Host-associated > Algae > Diatoms denotes diatoms acting as microbial hosts. The organism is the habitat; the taxon class is evidence about the host and remains an xref rather than the record identity. |
| leporid-associated environment | 217 | BACDIVE | Host-taxon reversal (#114): this was NOT_APPLICABLE on the reasoning that 'a host taxon is not a habitat'. That reasoning is wrong, and the corpus already contradicted it — the same kind of concept was treated as a habitat for Sponge, Nematoda, Reptilia, Mammals, Birds and Fish, which keep their own identity and a term request for an <X>-associated environment. Host-associated > Porifera was NOT_APPLICABLE while its own child Porifera > Sponge was a term request.An organism acting as a host IS a habitat: it is where the microbe lives, and ENVO models exactly this at plant-associated, animal-associated and fungi-associated environment. What is not a habitat is the TAXON TERM — a phylum is a class of organisms, not a place — so the taxon stays an xref (#99) and the concept keeps its own identity as a term-request candidate. NOT_APPLICABLE said the concept is not a habitat, which is a stronger and false claim. Category set to HOST_ASSOCIATED (#200): the row already claims ENVO:01001002 'animal-associated environment' as the nearest broader term, which is the claim that a living animal host defines the habitat, and every other record carrying that parent is HOST_ASSOCIATED. The category column was left blank here, so the seeder's default stood and five domestic-mammal hosts stayed in OTHER while their siblings did not. The reasoning above is unchanged. |
| chelicerate-associated environment | 169 | GOLD | Host-taxon reversal (#114): this was NOT_APPLICABLE on the reasoning that 'a host taxon is not a habitat'. That reasoning is wrong, and the corpus already contradicted it — the same kind of concept was treated as a habitat for Sponge, Nematoda, Reptilia, Mammals, Birds and Fish, which keep their own identity and a term request for an <X>-associated environment. Host-associated > Porifera was NOT_APPLICABLE while its own child Porifera > Sponge was a term request.An organism acting as a host IS a habitat: it is where the microbe lives, and ENVO models exactly this at plant-associated, animal-associated and fungi-associated environment. What is not a habitat is the TAXON TERM — a phylum is a class of organisms, not a place — so the taxon stays an xref (#99) and the concept keeps its own identity as a term-request candidate. NOT_APPLICABLE said the concept is not a habitat, which is a stronger and false claim. |
| inland saline or alkaline aquatic environment | 158 | BACDIVE, GOLD | Definition review (#110, #185): GOLD's node names the broad environment grouping its inland saline, alkaline and combined descendants, not a bare water quality. The earlier “quality, not a place” ruling confused the modifiers with the source concept and left a genuine 121-organism habitat undefined. ENVO:01000317 is the defensible existing genus. The inherited aquatic-biome edge is replaced by the curated definition because this source bin also contains operated settings such as solar salterns and fracking water. The node is disjunctive — saline OR alkaline OR both — and descendants that leak outside the intended inland scope remain independently curated. |
| annelid-associated environment | 150 | GOLD | Host-taxon reversal (#114): this was NOT_APPLICABLE on the reasoning that 'a host taxon is not a habitat'. That reasoning is wrong, and the corpus already contradicted it — the same kind of concept was treated as a habitat for Sponge, Nematoda, Reptilia, Mammals, Birds and Fish, which keep their own identity and a term request for an <X>-associated environment. Host-associated > Porifera was NOT_APPLICABLE while its own child Porifera > Sponge was a term request.An organism acting as a host IS a habitat: it is where the microbe lives, and ENVO models exactly this at plant-associated, animal-associated and fungi-associated environment. What is not a habitat is the TAXON TERM — a phylum is a class of organisms, not a place — so the taxon stays an xref (#99) and the concept keeps its own identity as a term-request candidate. NOT_APPLICABLE said the concept is not a habitat, which is a stronger and false claim. |
| reptile-associated environment | 133 | GOLD | xref-only review (#43): kg-microbe maps this to NCBITaxon:8504, which is OVER-NARROW — Lepidosauria excludes turtles and crocodilians, which Reptilia includes. The record carries no xref for it: this is a GOLD path and the mapping-table route did not apply, so the concept stays UNGROUNDED and the only trace of the mapping is upstream. Reported as kg-microbe#790. Path: Host-associated > Reptilia |
| green-alga-associated environment | 108 | GOLD | Non-habitat screen (#12): grounded EXACT to FOODON:03412502 'green algae', which FOODON uses for the TAXON — red algae is defined there as 'one of the oldest groups of eukaryotic algae, and one of the largest phyla' — not for a habitat. An organism group is not a place, and the GOLD path says host-associated, so the concept is the environment the alga provides. Same family as the sponge, nematode and reptile requests. The FOODON term is kept as an xref (#99), which records what the label matched without asserting the record is a phylum. |
| Rodentia-Other | 97 | BACDIVE | Residual-host review (#192): BacDive's live vocabulary places `Rodentia (Other)` under `#Host` as the sibling of `#Muridae (Mouse/Rat)`. It is a real animal-host environment, not NCIT:C17649 `Other`; that contentless lexical target remains rejected. ENVO:01001002 is genuinely broader and the category is HOST_ASSOCIATED. The source bucket means rodent hosts not assigned to the Muridae sibling, so it stays minted and separate: merging would erase the family-rank boundary, while requesting an ontology class defined by a mutable “everything else” exclusion would make its meaning change whenever BacDive adds a sibling. Hamsters and voles remain in scope despite vernacular mouse names; the attesting Actinobacillus capsulatus includes a reported rabbit-derived type strain outside Rodentia, so source assignment is preserved as evidence rather than treated as a taxonomic guarantee. |
| Biopsy | 95 | BACDIVE | CLOSE-grounding review (#12): the seeder made NCIT:C15189 'Biopsy Procedure' the identity of BacDive's 'Biopsy' category, 95 strains. A procedure is not a habitat — it is the act of taking the sample, not the place the organism lived, the same category error as grounding a record to an organism or a quality. The habitat is whichever tissue was biopsied, which BacDive does not say, so no term fits. The procedure term is kept as an xref (#99) to record what upstream matched without this repo asserting the record is a procedure. The record was CLINICAL while it carried the NCIT term and would fall to OTHER without one, because the category is inferred from the grounding; a biopsy is a clinical source whether or not a term fits, so the category is pinned rather than lost with the grounding. |
| felid-associated environment | 95 | BACDIVE | Host-taxon reversal (#114) reaching the last members of its own family (#194): this was NOT_APPLICABLE, which asserts the source concept is not a habitat. An organism acting as a host IS a habitat, and the corpus already says so for bovine, caprine, equid, leporid and suid, all minted with ENVO:01001002 'animal-associated environment' as parent and the organism term as an xref. Never curated on the question at all: the NOT_APPLICABLE was the seeder's automatic bacdive_non_habitat_target route firing on an NCBITaxon target, and #114's sweep did not reach this row. The taxon term is not the identity - a family is a class of organisms, not a place - so it stays an xref (#99) and the concept keeps its minted identity with a term request. Category HOST_ASSOCIATED: the host is living. |
| insect larva-associated environment | 94 | GOLD | Life-stage review (#112): carried UBERON:0002548 'larva' as a parent, reached by the ambiguous-leaf rule rather than the path — several GOLD paths end in the same leaf, so the ones that do not claim the term keep it as a parent. parent_habitats asserts the parent is BROADER, and a larva or embryo is a whole organism rather than a broader kind of place, so this is the same over-claim the identity cases had one level up. Kept as an xref (#99). Per the rule #114 settled: the whole host organism gets its own identity and an <X>-associated environment term; parts of a host ground to the anatomy term. |
| human skin lesion environment | 81 | GOLD | Stale-sweep review (#12): NCIT:C3824 'Lesion' matches the label now, but it is a pathological finding rather than a place, and the habitat here is the skin the lesion is on. The sweep's answer was right and its stated reason has stopped being true, so it is re-recorded with the reason that holds. Path: Host-associated > Mammals: Human > Integumentary system > Skin > Lesion |
| ascidian-associated environment | 79 | GOLD | Ascidians as host. BTO:0000090 is a biological-source term rather than a habitat; treated as the other host clades are, parented to animal-associated environment. ENVO term request. |
| red-alga-associated environment | 73 | GOLD | Non-habitat screen (#12): grounded EXACT to FOODON:03411743 'red algae', which FOODON uses for the TAXON — red algae is defined there as 'one of the oldest groups of eukaryotic algae, and one of the largest phyla' — not for a habitat. An organism group is not a place, and the GOLD path says host-associated, so the concept is the environment the alga provides. Same family as the sponge, nematode and reptile requests. The FOODON term is kept as an xref (#99), which records what the label matched without asserting the record is a phylum. |
| indoor air | 72 | GOLD | Indoor air. kg-microbe's mapping table pointed this at ENVO:01000855, which it labels 'indoor air' and ENVO labels 'area of mixed forest' — a different concept, now rejected by the label check. No indoor-air term exists in the vendored slice, so this is a genuine term request; parented to air. |
| macroalgal bed | 69 | GOLD | Non-habitat screen (#12): grounded EXACT to FOODON:03412266 'seaweed', defined there as 'a macroscopic, multicellular, marine algae (kingdom Protista)' — the organism, not the habitat. The concept under Environmental > Aquatic > Marine is the seaweed as a place microbes live, its surface and the bed it forms. No term for that is in the vendored slice, so the organism term is kept as an xref (#99) and this is a term-request candidate distinct from the host-taxon family: it wants a macroalgal-bed style environment term. |
| aquatic mammal-associated environment | 69 | BACDIVE | Host-taxon reversal (#114): this was NOT_APPLICABLE on the reasoning that 'a host taxon is not a habitat'. That reasoning is wrong, and the corpus already contradicted it — the same kind of concept was treated as a habitat for Sponge, Nematoda, Reptilia, Mammals, Birds and Fish, which keep their own identity and a term request for an <X>-associated environment. Host-associated > Porifera was NOT_APPLICABLE while its own child Porifera > Sponge was a term request.An organism acting as a host IS a habitat: it is where the microbe lives, and ENVO models exactly this at plant-associated, animal-associated and fungi-associated environment. What is not a habitat is the TAXON TERM — a phylum is a class of organisms, not a place — so the taxon stays an xref (#99) and the concept keeps its own identity as a term-request candidate. NOT_APPLICABLE said the concept is not a habitat, which is a stronger and false claim. Category set to HOST_ASSOCIATED (#110): the curated definition parents this to ENVO:01001002 'animal-associated environment', which is the claim that a living animal host defines the habitat, so OTHER would contradict the record's own parent. |
| aquatic macrophyte-associated environment | 66 | BACDIVE | Grounding-cohort review (#62): was FOODON:03401156 '50122200 - aquatic plants prepared/processed (gs1 gpc)', a UNSPSC commodity code for prepared food. An aquatic plant as an isolation source is a living host, not a prepared foodstuff, and no term in the slice names it. Category set to HOST_ASSOCIATED (#110): the curated definition parents this to ENVO:01001000 'environmental system determined by an organism' - a living macrophyte host - and 31 of the 33 records under that parent are HOST_ASSOCIATED. |
| lichen-associated environment | 66 | GOLD | Organism-identity screen (#109): grounded EXACT to FOODON:03412345 'lichen', which is a composite organism arising from algae or cyanobacteria living among fungal filaments — an organism, not a place. The screen that exists to catch exactly this reported 0 for months because it tested only NCIT and mesh ancestry and only the record's identity; widening it to UBERON:0000468 and to parent_habitats surfaced this family. The GOLD path says host-associated, so the concept is the environment the organism provides, which is the same family as the sponge, nematode and reptile term requests. The organism term is kept as an xref (#99) rather than an identity. |
| indoor dust | 65 | GOLD | Indoor dust is settled particulate matter in a built environment, not air. GOLD's Air branch is about where the sample came from, not what it is. |
| oyster-associated environment | 61 | GOLD | Organism-identity screen (#109): grounded EXACT to FOODON:03411224 'oyster', which is a bivalve mollusc — an organism, not a place. The screen that exists to catch exactly this reported 0 for months because it tested only NCIT and mesh ancestry and only the record's identity; widening it to UBERON:0000468 and to parent_habitats surfaced this family. The GOLD path says host-associated, so the concept is the environment the organism provides, which is the same family as the sponge, nematode and reptile term requests. The organism term is kept as an xref (#99) rather than an identity. |
| Core-sample | 60 | BACDIVE | Cohort review: the screen's known blind spot, caught by reading the corpus rather than the ranking. NCIT:C180316 "Nucleotide Sequence Sample Name" is a metadata field name, not a place; it shares the word "sample" with the subject, so it lands in the low-risk overlap bucket. A sediment or ice core is a real habitat and no term in the slice names it. |
| bivalve-associated environment | 59 | GOLD | Bivalves as host. FOODON:03412113 bivalve is a food product class, not a host organism, so it is the wrong kind of term entirely. Parented to animal-associated environment like the other host clades. ENVO term request. |
| sea urchin-associated environment | 53 | GOLD | Organism-identity screen (#109): grounded EXACT to FOODON:03412107 'sea urchin', which is an echinoderm — an organism, not a place. The screen that exists to catch exactly this reported 0 for months because it tested only NCIT and mesh ancestry and only the record's identity; widening it to UBERON:0000468 and to parent_habitats surfaced this family. The GOLD path says host-associated, so the concept is the environment the organism provides, which is the same family as the sponge, nematode and reptile term requests. The organism term is kept as an xref (#99) rather than an identity. |
| protist-associated environment | 43 | BACDIVE, GOLD | Protist-definition pass (#110): GOLD's Host-associated > Protists source denotes protists acting as microbial hosts. ENVO has no protist-associated child of ENVO:01001000 'environmental system determined by an organism' to ground to, and NCIT:C77914 'Protista' is a legacy taxon rather than a habitat identity, so it is retained only as an xref. The GOLD source is the merge survivor because it contributes an explicit Host-associated path and 40 organism assertions. |
| outdoor air | 42 | GOLD | Outdoor air. The mapping table pointed this at ENVO:01000829, which it labels 'outdoor air' and ENVO labels 'water vapour saturated air'. No outdoor-air term in the slice; parented to air. Term request. |
| amphibian-associated environment | 41 | GOLD | Host-taxon reversal (#114): this was NOT_APPLICABLE on the reasoning that 'a host taxon is not a habitat'. That reasoning is wrong, and the corpus already contradicted it — the same kind of concept was treated as a habitat for Sponge, Nematoda, Reptilia, Mammals, Birds and Fish, which keep their own identity and a term request for an <X>-associated environment. Host-associated > Porifera was NOT_APPLICABLE while its own child Porifera > Sponge was a term request.An organism acting as a host IS a habitat: it is where the microbe lives, and ENVO models exactly this at plant-associated, animal-associated and fungi-associated environment. What is not a habitat is the TAXON TERM — a phylum is a class of organisms, not a place — so the taxon stays an xref (#99) and the concept keeps its own identity as a term-request candidate. NOT_APPLICABLE said the concept is not a habitat, which is a stronger and false claim. |
| protozoan-associated environment | 32 | GOLD | Host-taxon reversal (#114): this was NOT_APPLICABLE on the reasoning that 'a host taxon is not a habitat'. That reasoning is wrong, and the corpus already contradicted it — the same kind of concept was treated as a habitat for Sponge, Nematoda, Reptilia, Mammals, Birds and Fish, which keep their own identity and a term request for an <X>-associated environment. Host-associated > Porifera was NOT_APPLICABLE while its own child Porifera > Sponge was a term request.An organism acting as a host IS a habitat: it is where the microbe lives, and ENVO models exactly this at plant-associated, animal-associated and fungi-associated environment. What is not a habitat is the TAXON TERM — a phylum is a class of organisms, not a place — so the taxon stays an xref (#99) and the concept keeps its own identity as a term-request candidate. NOT_APPLICABLE said the concept is not a habitat, which is a stronger and false claim. |
| Root-Tooth | 28 | BACDIVE | Cohort review: NCIT:C33446 'Root' is unqualified and reads as a plant root, not the root of a tooth. The slice has no tooth-root term. Real habitat, no term. |
| cooling tower | 26 | BACDIVE | Definition review: the existing cohort review correctly rejected NCIT:C48957 'Tower' as merely a structure of any kind and ENVO:03600002 'cooling water' as a medium rather than a site. BacDive's cooling-tower source denotes an open, recirculating, evaporative heat-rejection construction that needs its own HabitatMech definition. |
| fish skin lesion environment | 23 | GOLD | Stale-sweep review (#12): the fish skin-lesion concept, same as the human one — NCIT's 'Lesion' is a finding, not a place. Path: Host-associated > Fish > Integumentary system > Skin > Lesion |
| tunicate-associated environment | 23 | GOLD | Host-taxon reversal (#114): this was NOT_APPLICABLE on the reasoning that 'a host taxon is not a habitat'. That reasoning is wrong, and the corpus already contradicted it — the same kind of concept was treated as a habitat for Sponge, Nematoda, Reptilia, Mammals, Birds and Fish, which keep their own identity and a term request for an <X>-associated environment. Host-associated > Porifera was NOT_APPLICABLE while its own child Porifera > Sponge was a term request.An organism acting as a host IS a habitat: it is where the microbe lives, and ENVO models exactly this at plant-associated, animal-associated and fungi-associated environment. What is not a habitat is the TAXON TERM — a phylum is a class of organisms, not a place — so the taxon stays an xref (#99) and the concept keeps its own identity as a term-request candidate. NOT_APPLICABLE said the concept is not a habitat, which is a stronger and false claim. |
| echinoderm-associated environment | 21 | GOLD | Host-taxon reversal (#114): this was NOT_APPLICABLE on the reasoning that 'a host taxon is not a habitat'. That reasoning is wrong, and the corpus already contradicted it — the same kind of concept was treated as a habitat for Sponge, Nematoda, Reptilia, Mammals, Birds and Fish, which keep their own identity and a term request for an <X>-associated environment. Host-associated > Porifera was NOT_APPLICABLE while its own child Porifera > Sponge was a term request.An organism acting as a host IS a habitat: it is where the microbe lives, and ENVO models exactly this at plant-associated, animal-associated and fungi-associated environment. What is not a habitat is the TAXON TERM — a phylum is a class of organisms, not a place — so the taxon stays an xref (#99) and the concept keeps its own identity as a term-request candidate. NOT_APPLICABLE said the concept is not a habitat, which is a stronger and false claim. |
| Dust-Ash | 20 | BACDIVE | Definition review (#252, #253): the committed Dust-Ash report agrees that neither ENVO:00002008 'dust' nor ENVO:02000090 'ash' can be adopted as the identity because each drops the other half of BacDive's #Engineered > #Waste > #Dust (Ash) bucket. ENVO:01000814 'solid environmental material' is the least common vendored parent of the two halves and is attached as a broad placement until BacDive strain-level isolation text can split the dust-like and ash-like strains upstream; category pinned to ENGINEERED because MISO files the source under #Engineered > #Waste. |
| waste gas | 20 | BACDIVE | Definition review: ENVO:01001155 'astrogeological gas' remains a false lexical hit through its bare synonym 'gas'. BacDive's MISO path places #Waste gas under #Engineered > #Waste; the source denotes confined anthropogenic gaseous effluent, and no vendored ontology term names that habitat. ENVO:01000797 'gaseous environmental material' is the true genus for a term request; ENVO:00002267 'industrial waste material' stays a near-miss because agricultural and municipal waste gases need not be manufacturing waste. |
| dinoflagellate-associated environment | 19 | GOLD | Non-habitat screen review (#108): Host-associated > Protists > Dinoflagellates denotes dinoflagellates acting as microbial hosts. The organism is the habitat concept; the taxon term remains an xref rather than becoming the record identity. |
| sea cucumber-associated environment | 17 | GOLD | Organism-identity screen (#109): grounded EXACT to FOODON:02022154 'sea cucumber', which is an echinoderm — an organism, not a place. The screen that exists to catch exactly this reported 0 for months because it tested only NCIT and mesh ancestry and only the record's identity; widening it to UBERON:0000468 and to parent_habitats surfaced this family. The GOLD path says host-associated, so the concept is the environment the organism provides, which is the same family as the sponge, nematode and reptile term requests. The organism term is kept as an xref (#99) rather than an identity. |
| active sourdough starter | 15 | GOLD | The committed sourdough report kept this as a real habitat with no defensible identity term: FOODON:03302481 'sourdough bread' is the baked product after the microbial habitat has ended, and the unvendored FoodOn sourdough-starter classes are commodity or facet-bundle terms that over-claim relative to GOLD's Engineered > Food production > Sourdough source. ENVO:03600040 'fermentation starter' is a true broader parent because sourdough is a maintained flour-water starter used to acidify and leaven bread dough. Path: Engineered > Food production > Sourdough |
| amoebozoan-associated environment | 13 | GOLD | Non-habitat screen review (#108): Host-associated > Amoebozoa denotes an amoebozoan organism acting as a microbial host. An external taxon term supports the host identity but is external to the committed ontology slice, so it is documented here rather than asserted unverifiably. |
| serpentinization-hosted carbonate hydrothermal vent chimney | 12 | GOLD | Definition research for Carbonate traced the inspected GOLD organism rows to Prony Hydrothermal Field carbonate chimneys, not to soda-lake water or to carbonate ion as a habitat. The leaf denotes a serpentinization-hosted brucite/carbonate hydrothermal chimney; ENVO:01000129 is the term-request genus, ENVO:01000053 is related ultramafic vent context rather than an identity or parent, and alkaline-water and carbonate-chemistry terms describe the venting fluid or its chemistry rather than the sampled chimney. GOLD's Non-marine Saline and Alkaline placement is a source classification artifact here because the chimneys stand in shallow marine and intertidal settings. |
| peat moss-associated environment | 11 | GOLD | Report confirms GOLD Peat moss as a living Sphagnum gametophore host habitat. mesh:D044003 remains xref because Sphagnopsida is a taxon; ENVO:01001001 already provides the true plant-associated parent. ENVO sphagnum bog, peat soil, peatland and area of moss-dominated vegetation are ecosystem, decomposed-substrate or landcover false matches. ENVO:01001057 is a near miss because it includes dead plant matter and sits outside the host-associated branch. Path: Host-associated > Plants > Peat moss. |
| platyhelminth-associated environment | 11 | GOLD | Non-habitat screen review (#108): Host-associated > Invertebrates > Platyhelminthes denotes flatworms acting as microbial hosts. An external taxon term supports that reading but is not present in the committed slice, so it is not asserted as an xref. |
| tuberculous granuloma | 11 | PREGO | Item-level tubercle report read in full before definition authoring. The earlier disjoint decision stands: BTO:0002173 is a Schistosoma body-part homonym, and the UBERON and PO tubercle terms name generic normal anatomical protrusions and plant protuberances, while PREGO's source string points at a mycobacterial tubercle. No vendored ontology term names the infectious granulomatous lesion itself, so the record remains UNGROUNDED. Category set to HOST_ASSOCIATED because this habitat is formed within host tissue rather than an external OTHER source. |
| persistent organic pollutant bioremediation material | 9 | GOLD | Variant-match review (#12): the variant route strips GOLD's parenthetical and reaches UBERON:0002622 'preoptic periventricular nucleus', a structure in the BRAIN, for a class of industrial chemicals. The path is Engineered > Bioremediation > Persistent organic pollutants (POP), so the habitat is the contaminated material being remediated; the pollutants themselves are chemicals rather than places, and no term in the slice names the habitat. Path: Engineered > Bioremediation > Persistent organic pollutants (POP) |
| leaf-or-stem spot lesion environment | 5 | BACDIVE | Cohort review: a leaf-or-stem lesion. PO:0009047 'stem' drops the leaf and is also the target of 'Rot-Root,Stem', so adopting it would merge two different plant diseases onto one record. |
| anaerobic wastewater treatment reactor | 3 | GOLD | Stale-sweep review (#84): the variant search reaches PATO:0001456 'anaerobic' by taking the parenthetical from 'Dissolved organics (anaerobic)'. A quality is not a habitat — the call already recorded for Acidic, Humid, Arid and the climatic zones — and the habitat here is the wastewater, not its oxygen state. The sweep's answer stands; its stated reason no longer does. Path: Engineered > Wastewater > Nutrient removal > Dissolved organics (anaerobic) |
| brown algal embryo | 3 | GOLD | Life-stage review (#112): carried UBERON:0000922 'embryo' as a parent, reached by the ambiguous-leaf rule rather than the path — several GOLD paths end in the same leaf, so the ones that do not claim the term keep it as a parent. parent_habitats asserts the parent is BROADER, and a larva or embryo is a whole organism rather than a broader kind of place, so this is the same over-claim the identity cases had one level up. Kept as an xref (#99). Per the rule #114 settled: the whole host organism gets its own identity and an <X>-associated environment term; parts of a host ground to the anatomy term. |
| insect nymph-associated environment | 3 | GOLD | Life-stage host review (#276): BTO:0000954 'nymph' names an immature insect organism at a stage rather than an environment determined by that organism, the same entity-type mismatch already recorded for Larva, Pupa, Prepupa, and Embryo under #112/#114. The GOLD Nymph/Instar source stays minted as a whole-host insect habitat and keeps BTO:0000954 only as an xref so all insect life-stage hosts follow one rule. |
| methane bioremediation material | 2 | GOLD | Definition research for Engineered > Bioremediation > Hydrocarbon > Methane kept the record ungrounded: GOLD names the remediated methane contaminant rather than a sampled chemical, and CHEBI:16183 exactly identifies methane but is a chemical retained only as an unvendored xref. A material term is requested under ENVO:00010483 'environmental material'; parent_mode=REPLACE drops the inherited Hydrocarbon parent because that source node is a chemical class, not a microbial habitat. |
| built heritage structure | 2 | GOLD | Committed Monument report rechecked the stale #67 conclusion: ENVO:00000359 'natural monument' remains a false lexical hit because GOLD's Engineered > Built environment > Monument source denotes built heritage, but the slice does contain ENVO:02000132 'constructed monument'. That term is an xref, not identity or parent, because its memorial-function definition overlaps but does not subsume temples, grottoes, cathedral facades, Stone, and Interior wall; the term request supplies ENVO:00000070 'human construction' as the true genus. |
| oomycete-associated environment | 2 | GOLD | Non-habitat screen review (#108): Host-associated > Protists > Oomycetes denotes oomycetes acting as microbial hosts. NCBITaxon:4762 'Oomycota' is retained as an exact taxon xref; the taxon class is evidence about the host, not the habitat identity. |
| insect prepupa-associated environment | 2 | GOLD | Life-stage review (#112), applying the rule #114 settled: the whole host ORGANISM gets its own identity plus an <X>-associated environment term, while PARTS of a host ground to the anatomy term as gut, skin and lung already do. A larva, pupa, prepupa or embryo is the whole organism at a stage, not a part of one, so UBERON:0003142 'prepupa' is the organism rather than the place — the same shape as Mollusca, Porifera and the host clades. Kept as an xref (#99); the concept keeps its own identity as a term-request candidate.This is the line that makes both calls fall out of one rule, rather than an exception for terms that happen to live in UBERON: a cocoon is a STRUCTURE an insect builds and stays grounded, because it is not the organism. |
| root-or-stem rot environment | 2 | BACDIVE | Cohort review: root-or-stem rot. Same PO:0009047 'stem' merge as the leaf-spot source, and the same objection — the dropped alternative is half the concept. |
| gulf | 1 | GOLD | Non-habitat screen review (#108): Environmental > Aquatic > Marine > Gulf unambiguously denotes the marine water body setting. The external chemical term label collision is unrelated to this path and is not retained as an xref. |
| marine rubber waste | 1 | GOLD | Non-habitat screen review (#108): Environmental > Aquatic > Marine > Waste > Rubber describes rubber waste as a colonisable substrate in a marine setting. It is a physical habitat, not a claim that CHEBI's chemical class is a place; the external chemical term is not in the committed slice. |
| Thalassic | 1 | GOLD | ITEM identity assessment (#1572): GOLD3976 classifies a thalassic saline sampling environment, not the physical quality ENVO:01001667. Official ENVO a2455d1a77e46bb8a664d65a157166b539269042 places that term beneath physical quality; retain it only as an xref. GOLD's classification documentation and the committed aquatic-biome/lagoon/saline-water triad support an environmental source, but one sample does not establish a universal lagoon, whole water body or water-material identity. Preserve the minted source habitat without inventing a definition or a replacement genus. The source-context saline-water-body contribution is separately excluded. Path: Environmental > Aquatic > Non-marine Saline and Alkaline > Saline > Thalassic |
| buffer solution | 1 | GOLD | Non-habitat screen review (#108): Engineered > Industrial production > Chemical products > Buffer denotes a manufactured buffer solution or product, a physical fluid material in which microbes can occur. An external chemical term identifies the chemical role but is not in the committed slice. |
| oil or gas pipeline network | 1 | GOLD | Definition research for Oil/Gas pipeline found ENVO:03600014 'pipeline network' as a true broader term and ENVO:03600012 'oil pipeline network' as a narrower related term that covers only the oil half and adds a consumer-destination constraint. The GOLD leaf denotes oil and natural-gas pipeline systems, including gathering and production lines that need not transport material to consumers, so it keeps a minted identity and carries the oil-pipeline term only as an xref. |
| xylene bioremediation material | 1 | GOLD | Non-habitat screen review (#108): Engineered > Bioremediation > Hydrocarbon > Xylene denotes a xylene-contaminated engineered environment undergoing remediation, not pure xylene as the habitat. An external chemical term supplies the contaminant identity but is outside the committed slice. |
| endosymbiotic bacterium-associated environment | 1 | GOLD | Host-taxon reversal (#114): this was NOT_APPLICABLE on the reasoning that 'a host taxon is not a habitat'. That reasoning is wrong, and the corpus already contradicted it — the same kind of concept was treated as a habitat for Sponge, Nematoda, Reptilia, Mammals, Birds and Fish, which keep their own identity and a term request for an <X>-associated environment. Host-associated > Porifera was NOT_APPLICABLE while its own child Porifera > Sponge was a term request.An organism acting as a host IS a habitat: it is where the microbe lives, and ENVO models exactly this at plant-associated, animal-associated and fungi-associated environment. What is not a habitat is the TAXON TERM — a phylum is a class of organisms, not a place — so the taxon stays an xref (#99) and the concept keeps its own identity as a term-request candidate. NOT_APPLICABLE said the concept is not a habitat, which is a stronger and false claim. |
| molluscan gill extracellular environment | 1 | GOLD | Non-habitat screen review (#108): Host-associated > Mollusca > Respiratory system > Gills > Extracellular denotes the extracellular compartment of gill tissue, a real microbial habitat. GO:0005615 'extracellular space' describes the spatial compartment but is not itself a microbial-habitat identity, so it is retained only as an xref. |
| molluscan gill intracellular environment | 1 | GOLD | Non-habitat screen review (#108): the full path Host-associated > Mollusca > Respiratory system > Gills > Intracellular denotes the intracellular compartment of gill tissue, a real microbial habitat. The GO term describes the spatial compartment but is not itself a microbial-habitat identity, so it is retained only as an xref. |
| nauplius-associated environment | 1 | GOLD | Definition research for Larva: Nauplius corrected the reason to stay UNGROUNDED: BTO:0000915 'nauplius' names the crustacean larva exactly, but it is still a whole organism at a life stage rather than an environmental system determined by that organism. The GOLD concept keeps a minted habitat identity under the same #112/#114 whole-organism rule used for Larva, Pupa, Prepupa, and Embryo; the BTO organism term is retained only as an xref. |
| mammalian nasal discharge material | 1 | GOLD | Non-habitat screen review (#108): the path ends Mammals > Respiratory system > Nasal cavity > Nasal discharge, so the concept is the physical secretion carrying microbes rather than the phenotype abstractly. An external phenotype term supports the clinical context but is not in the committed slice. |
| aerial plant surface environment | 1 | GOLD | Disjoint-grounding review (#62): was UBERON:0002416 'integumental system', an ANIMAL organ system, for a plant leaf surface — matched across kingdoms on a synonym. The slice has no plain plant-surface or phyllosphere term; the nearest, ENVO:01001032, is specifically a biofilm on one. Path: Host-associated > Plants > Phyllosphere > Surface |
| aquifer rock or sediment | 1 | GOLD | Definition research for Rock core/Sediment retained the GOLD Aquifer parent and confirmed that ENVO:00012408 'aquifer' is a geologic body rather than the rock-or-sediment material that composes it. The GOLD leaf denotes in situ saturated aquifer matrix rather than the recovered core cylinder, so aquifer is retained only as an xref for its part-of context and ENVO:00002007 sediment is still rejected as a parent because it drops the rock half of the source concept. |
| Biofouling | 0 | GOLD | Process screen (#127): carried ENVO:06105023 'biofouling' as a parent, which ENVO defines as 'a FOULING PROCESS during which biological matter accumulates on a solid surface' and files under environmental system process. parent_habitats asserts the parent is a broader HABITAT, so the corpus was claiming a habitat is-a process — the thing MIxS rules out in the same sentence that rules out organisms and groups of organisms, and the reason that sentence is now quoted in CLAUDE.md. The concept is the fouling layer, not the fouling. It reached the term through the ambiguous-leaf rule: the deep-subsurface groundwater path, and three of the four Biofouling paths tie at the same depth so none claimed it. Kept as an xref (#99), which records what upstream matched without asserting the record is a process. Not grounded to ENVO:00002034 'biofilm' either: biofouling includes macrofouling such as barnacles and tube worms, so biofilm is narrower than the concept rather than broader. |
| Biofouling | 0 | GOLD | Process screen (#127): carried ENVO:06105023 'biofouling' as a parent, which ENVO defines as 'a FOULING PROCESS during which biological matter accumulates on a solid surface' and files under environmental system process. parent_habitats asserts the parent is a broader HABITAT, so the corpus was claiming a habitat is-a process — the thing MIxS rules out in the same sentence that rules out organisms and groups of organisms, and the reason that sentence is now quoted in CLAUDE.md. The concept is the fouling layer, not the fouling. It reached the term through the ambiguous-leaf rule: the freshwater path, and three of the four Biofouling paths tie at the same depth so none claimed it. Kept as an xref (#99), which records what upstream matched without asserting the record is a process. Not grounded to ENVO:00002034 'biofilm' either: biofouling includes macrofouling such as barnacles and tube worms, so biofilm is narrower than the concept rather than broader. |
| Biofouling | 0 | GOLD | Process screen (#127): carried ENVO:06105023 'biofouling' as a parent, which ENVO defines as 'a FOULING PROCESS during which biological matter accumulates on a solid surface' and files under environmental system process. parent_habitats asserts the parent is a broader HABITAT, so the corpus was claiming a habitat is-a process — the thing MIxS rules out in the same sentence that rules out organisms and groups of organisms, and the reason that sentence is now quoted in CLAUDE.md. The concept is the fouling layer, not the fouling. It reached the term through the ambiguous-leaf rule: the non-marine saline and alkaline path, and three of the four Biofouling paths tie at the same depth so none claimed it. Kept as an xref (#99), which records what upstream matched without asserting the record is a process. Not grounded to ENVO:00002034 'biofilm' either: biofouling includes macrofouling such as barnacles and tube worms, so biofilm is narrower than the concept rather than broader. |
| Biofouling | 0 | GOLD | Process screen (#127): carried ENVO:06105023 'biofouling' as a parent, which ENVO defines as 'a FOULING PROCESS during which biological matter accumulates on a solid surface' and files under environmental system process. parent_habitats asserts the parent is a broader HABITAT, so the corpus was claiming a habitat is-a process — the thing MIxS rules out in the same sentence that rules out organisms and groups of organisms, and the reason that sentence is now quoted in CLAUDE.md. The concept is the fouling layer, not the fouling. It reached the term through the ambiguous-leaf rule: the marine path, and three of the four Biofouling paths tie at the same depth so none claimed it. Kept as an xref (#99), which records what upstream matched without asserting the record is a process. Not grounded to ENVO:00002034 'biofilm' either: biofouling includes macrofouling such as barnacles and tube worms, so biofilm is narrower than the concept rather than broader. |
| Subterranean lake | 0 | GOLD | ITEM scope assessment (#1562): the freshwater-qualified source denotes an underground lake, not fresh-water material. Current ENVO:00000058 covers below-surface lakes; the exact GOLD path and its local-scale annotation support this genus, not exact equivalence with every underground lake. Retain the qualified minted identity and use an explicit broader parent without a source mapping predicate (#1398). GOLD4561/4562 and Gs0142421 support one path; two bulk/API samples from one study are not organism counts. The guarded source-parent exclusion separately removes ENVO:00002011. No universal taxa, chemistry or definition is inferred from the sampled cohort. Path: Environmental > Aquatic > Freshwater > Subterranean lake |
| Subterranean lake | 0 | GOLD | ITEM scope assessment (#1563): the deep-subsurface source denotes an underground lake, with an unresolved depth qualifier rather than proven exact coextension with ENVO:00000058. The source path and local-scale annotation support that broader genus. Retain the source identity and independent Deep subsurface parent; use explicit parent placement without introducing the implicit mapping endpoints in #1398. GOLD7667/7668 has 97 bulk biosamples versus 96 API samples from one study; Gs0111485 spans 25 paths, whose observations must not be transferred. Freshwater cohort annotations do not make the whole source class freshwater. No numeric depth cutoff or authored definition is asserted. Path: Environmental > Aquatic > Deep subsurface > Subterranean lake |
| Subtidal zone sediment | 0 | GOLD | ITEM assessment (#1567). Path: Environmental > Aquatic > Marine > Neritic zone/Coastal water > Subtidal zone sediment. This is a qualified marine sediment habitat, not coastal sea-water material. ENVO:03000033 (marine sediment) is a strictly broader genus verified against the current official ENVO ontology and committed slice; no exact term is established for this qualified source. Retain the minted identity and omitted organism count, with no source-mapping predicate. A guarded exclusion removes only the separate coastal-water context edge. No generic-sediment merge, universal grain size, depth, taxa or transferred biosample count is asserted. Supersedes the unassessed August 12 CLASS rationale, preserved in append-only session provenance. |
| air scrubber | 0 | GOLD | An air scrubber is a piece of equipment. GOLD files it under Air because the sample is scrubber air, but the habitat named by this leaf is the device, which belongs with the other built and managed environments. |
| air scrubber biofilm | 0 | GOLD | A biofilm growing inside an air scrubber. Whatever GOLD's branch, a biofilm is not air; it is a community on engineered equipment. |
| indoor artificial water channel system | 0 | GOLD | GOLD's 'Indoor' node. The mapping table pointed it at ENVO:01000856, which it labels 'indoor environment' and ENVO labels 'temperate marginal sea biome'. No indoor-environment term in the vendored slice. Term request. |
| solid manufactured material | 0 | GOLD | Stale-sweep review (#12): NCIT:C48187 'Material' matches the label and carries none of the meaning — a residual bucket like the NCIT 'Other' and 'Part' terms already refused in #43. Path: Engineered > Industrial production > Engineered product > Material |
| built heritage stone material | 0 | GOLD | Stale-sweep review (#12): NCIT:C35708 'Stone' matches the label, but the path is Built environment > Monument > Stone, and NCIT's term is not the building material. Stonework is a real habitat with no term in the slice. Path: Engineered > Built environment > Monument > Stone |
| subway environment | 0 | GOLD | Narrowed-grounding review (#67): was ENVO:03501109 'subway train'. GOLD's path is Engineered > Built environment > City > Subway, which is the system or the station rather than the rolling stock; the slice has train terms but nothing for the subway environment itself. |
| artificial water channel system | 0 | GOLD | Item-level review from the committed Indoor deep-research report: GOLD's Engineered > Artificial ecosystem > Water channel system source denotes artificial stream-channel vivaria, not built-environment canals, plumbing, bioreactors, or lab-enrichment cultures; its children are Indoor, Outdoor, and Indoor > Biofilm. No ENVO term names a laboratory or outdoor recirculating water-channel system. ENVO:00010622 'vivarium' is broader, ENVO:00000121 'artificial channel' and ENVO:00000079 'flume' overclaim civil-engineering landform or canal semantics, and ENVO:01000620 'mesocosm' is defined as embedded within a natural environment. Term request. |
| accessory nidamental gland | 0 | GOLD | Variant-match review (#12): the variant route reaches UBERON:0002788 'anterior nuclear group', a region of the THALAMUS, for a mollusc reproductive gland — a match with nothing behind it. UBERON has no nidamental gland term; CEPH:0000001 'accessory nidamental gland' exactly names the organ but is retained only as an inactive, unvendored anatomy xref (#290). Path: Host-associated > Mollusca > Reproductive system > Accessory nidamental gland |
| insect air sac | 0 | GOLD | Sibling-path review (#12): grounding the bird 'Air sacs' concept made this one's sweep stale, but UBERON's air sacs are ALL vertebrate — UBERON:0009060 is defined as extensions of the lungs of birds, and every sibling term is avian or cetacean. The path is Insects > Respiratory system > Trachea, where an air sac is a tracheal dilation. UBERON has no insect air sac. Path: Host-associated > Arthropoda: Insects > Respiratory system > Trachea > Air sacs |
| compartment 1 of camelid stomach | 0 | GOLD | Variant-match review (#12): the variant route reaches UBERON:0001092 'vertebral bone 1'. The path is Mammals > Digestive system > Stomach, so C1 is the first compartment of a camelid stomach — the same reading already recorded for C2 and C3. The slice has no term for it. Path: Host-associated > Mammals > Digestive system > Stomach > C1/Glandular saccules |
| compartment 2 of camelid stomach | 0 | GOLD | Disjoint-grounding review (#62): was UBERON:0001093 'vertebral bone 2'. The path is Host-associated > Mammals > Digestive system > Stomach > C2, so C2 is the second compartment of a camelid stomach, not a neck vertebra. The slice has no term for it. Path: Host-associated > Mammals > Digestive system > Stomach > C2 |
| compartment 3 of camelid stomach | 0 | GOLD | Disjoint-grounding review (#62): was UBERON:0002960 'central oculomotor nucleus', a brainstem structure. Same as C2 — the path is Digestive system > Stomach > C3, a camelid stomach compartment. Path: Host-associated > Mammals > Digestive system > Stomach > C3 |
| Ceros | 0 | GOLD | Deep-research follow-up: retained CONFIRM_UNGROUNDED after resolving the false FOODON:03413986 'cero' variant; GOLD places Ceros beside Horn and Pronghorn under Mammals > Integumentary system, but Ceros has no attested standalone anatomical usage. UBERON:0006967 'horn' fits if Ceros is a duplicate of the GOLD Horn sibling, while grounding to it would over-claim a living bony core if Ceros instead denotes rhinoceros horn, so the horn term is retained only as an xref. Path: Host-associated > Mammals > Integumentary system > Ceros |
| Embryo | 0 | GOLD | Life-stage review (#112): carried UBERON:0000922 'embryo' as a parent, reached by the ambiguous-leaf rule rather than the path — several GOLD paths end in the same leaf, so the ones that do not claim the term keep it as a parent. parent_habitats asserts the parent is BROADER, and a larva or embryo is a whole organism rather than a broader kind of place, so this is the same over-claim the identity cases had one level up. Kept as an xref (#99). Per the rule #114 settled: the whole host organism gets its own identity and an <X>-associated environment term; parts of a host ground to the anatomy term. |
| fish embryo-associated environment | 0 | GOLD | Life-stage review (#112), applying the rule #114 settled: the whole host ORGANISM gets its own identity plus an <X>-associated environment term, while PARTS of a host ground to the anatomy term as gut, skin and lung already do. A larva, pupa, prepupa or embryo is the whole organism at a stage, not a part of one, so UBERON:0000922 'embryo' is the organism rather than the place — the same shape as Mollusca, Porifera and the host clades. Kept as an xref (#99); the concept keeps its own identity as a term-request candidate.This is the line that makes both calls fall out of one rule, rather than an exception for terms that happen to live in UBERON: a cocoon is a STRUCTURE an insect builds and stays grounded, because it is not the organism. |
| gaster environment | 0 | GOLD | Disjoint-grounding review (#62) remains correct: GOLD's Host-associated > Arthropoda: Insects > Abdomen > Metasoma > Gaster path denotes the gaster of an apocritan hymenopteran, not UBERON:0000945 'stomach' or BTO:0001307 'stomach'. Definition research confirmed it is an intact body-region sampling unit containing gut, glandular, reproductive, intracellular, and cuticular niches; HAO:0000369 'gaster' is an exact unvendored anatomy match retained only as an xref until HAO is vendored or ENVO gains a gaster environment class. |
| crustacean larva-associated environment | 0 | GOLD | Life-stage review (#112): carried UBERON:0002548 'larva' as a parent, reached by the ambiguous-leaf rule rather than the path — several GOLD paths end in the same leaf, so the ones that do not claim the term keep it as a parent. parent_habitats asserts the parent is BROADER, and a larva or embryo is a whole organism rather than a broader kind of place, so this is the same over-claim the identity cases had one level up. Kept as an xref (#99). Per the rule #114 settled: the whole host organism gets its own identity and an <X>-associated environment term; parts of a host ground to the anatomy term. |
| zoea-associated environment | 0 | GOLD | Life-stage review (#112): carried UBERON:0002548 'larva' as a parent, reached by the ambiguous-leaf rule rather than the path — several GOLD paths end in the same leaf, so the ones that do not claim the term keep it as a parent. parent_habitats asserts the parent is BROADER, and a larva or embryo is a whole organism rather than a broader kind of place, so this is the same over-claim the identity cases had one level up. Kept as an xref (#99). Per the rule #114 settled: the whole host organism gets its own identity and an <X>-associated environment term; parts of a host ground to the anatomy term. |
| metasoma environment | 0 | GOLD | Gaster definition research also reviewed this parent source: GOLD's Host-associated > Arthropoda: Insects > Abdomen > Metasoma path denotes an apocritan hymenopteran abdominal tagma and is a real body-region habitat, not UBERON:0000916 'abdomen' or a chelicerate metasoma. No vendored ENVO, UBERON, FOODON, BTO, or PO term names a metasoma environment; HAO:0000626 'metasoma' is an exact unvendored anatomy match retained only as an xref until HAO is vendored or ENVO gains an environment class. |
| insect pupa-associated environment | 0 | GOLD | Life-stage review (#112), applying the rule #114 settled: the whole host ORGANISM gets its own identity plus an <X>-associated environment term, while PARTS of a host ground to the anatomy term as gut, skin and lung already do. A larva, pupa, prepupa or embryo is the whole organism at a stage, not a part of one, so UBERON:0003143 'pupa' is the organism rather than the place — the same shape as Mollusca, Porifera and the host clades. Kept as an xref (#99); the concept keeps its own identity as a term-request candidate.This is the line that makes both calls fall out of one rule, rather than an exception for terms that happen to live in UBERON: a cocoon is a STRUCTURE an insect builds and stays grounded, because it is not the organism. |
| stingless bee cerumen | 0 | GOLD | Definition research for Beehive: Cerumen kept the record ungrounded: GOLD's cerumen denotes the wax-and-propolis construction material of stingless-bee nests, not UBERON:0002297 'cerumen' from the external auditory canal, and the vendored slice has wax and resin ingredients but no term for their Meliponini mixture. A material term is requested under ENVO:00010483 'environmental material'; parent_mode=REPLACE drops the source-derived Insects nest parent because cerumen is a nest component, not a kind of nest. |
| eutric leptosol | 0 | GOLD | Soil-classification review: 'Eutric' is a WRB QUALIFIER (base saturation >=50%), not a reference soil group, so there is no term for it and there should not be — the same reading already recorded for Acidic, Humid, Arid and the climatic zones. The concept the path names is a eutric leptosol, which is a real habitat, and ENVO:00002241 'leptosol' is already attached as its parent. Confirmed rather than grounded. Path: Environmental > Terrestrial > Soil > Leptosol > Eutric |
| cave spicule | 0 | GOLD | Variant-match review (#12): the variant route reaches UBERON:3010830 'spicule', which is animal anatomy. The path is Terrestrial > Deep subsurface > Cave, where a spicule is a mineral speleothem — a homonym across kingdoms of the kind that put Coral on a fish. Path: Environmental > Terrestrial > Deep subsurface > Cave > Spicules |