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update HACCP_term regex to required FOODON, add multivalue example #802

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update HACCP_term regex to required FOODON, add multivalue example #802

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update HACCP_term regex to required FOODON, add multivalue example
mslarae13 Jun 14, 2024
e8ee863
abs_air_humidity description had an extra `\n`
mslarae13 Jun 14, 2024
159394a
clean up unnecessary new lines `\n` in descriptions
mslarae13 Jun 18, 2024
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17 changes: 6 additions & 11 deletions src/mixs/schema/mixs.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -3703,13 +3703,14 @@ slots:
title: Hazard Analysis Critical Control Points (HACCP) guide food safety term
examples:
- value: tetrodotoxic poisoning [FOODON:03530249]
- value: tetrodotoxic poisoning[FOODON:03530249]; neurotoxic shellfish poisoning[FOODON:03530246]
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Copilot AI Mar 11, 2026

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The new multi-value example uses ; as a delimiter and omits the space before [ (e.g., poisoning[FOODON:...]). In this schema, multi-term free-text fields typically document/illustrate pipe-separated values (|), e.g. dietary_claim_use description (around mixs.yaml:5761-5763) and animal_feed_equip example ...|... (around mixs.yaml:4216). Consider updating this example to use | and the canonical termLabel [TERM:ID] spacing, or explicitly document that ; and optional spacing are intended for HACCP_term.

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keywords:
- food
- term
slot_uri: MIXS:0001215
multivalued: true
range: string
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$
pattern: ^.+\s*\[FOODON:\d+\](;\s*\[FOODON:\d+\])*$
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@mslarae13 mslarae13 Jun 14, 2024

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This regex requires FOODON ontology. Is this what we want?

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@mslarae13 mslarae13 Jun 28, 2024

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@turbomam @only1chunts

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@turbomam turbomam Jul 9, 2024

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Thanks! Please use the pattern ^(\S[^\r\n]*) [FOODON:\d{7,8}]$ instead of ^.+\s*\[FOODON:\d+\](;\s*\[FOODON:\d+\])*$ or see my notes on dynamic enumerations.

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@turbomam turbomam Jul 9, 2024

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Did you intentionally remove the white-space between the label and the term id? I don't think that's consistent with other ontology term patterns in MIxS

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@mslarae13 mslarae13 Jul 9, 2024 •
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@turbomam
For the white space, do you mean if it should be "lead poisoning [FOODON:03530243]" vs "lead poisoning[FOODON:03530243]"

So, the white space is supposed to be there? I thought I had it set to be valid with or without it... does it matter? If so, I'll make sure I correct it. Just tell me which is correct.

Looking at the submission schema the white space should be there. So I can make that update to the regex.

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@mslarae13 mslarae13 Jul 9, 2024 •
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From your comment here : #802 (comment)

^(\S[^\r\n]*) [FOODON:\d{7,8}]$

I f we want to use pattern-only validation, I suggest we go with that.

That regex ^(\S[^\r\n]*) [FOODON:\d{7,8}]$
is showing me that "lead poisoning [FOODON:03530243]" is invalid... :(

... are you sure that's right?? Or am I missing something about the formatting of the value for "lead poisoning [FOODON:03530243]" ?

I think it needs to be ^.+\s*\[FOODON:\d{7,8}]$

(https://www.ebi.ac.uk/ols4/ontologies/foodon/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FFOODON_03530221)

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@mslarae13 mslarae13 Jul 9, 2024

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Screenshot 2024-07-09 at 4 53 27 PM Screenshot 2024-07-09 at 4 53 40 PM

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@mslarae13 mslarae13 Dec 3, 2024 •
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decision, the regex in the 2nd image is good.

I'll test this and confirm then finish this PR.

Discussed 12/03
pattern vs structured_pattern : we have this for some of the more generic term label and term IDs.
Look for "settings" section in schema.

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@turbomam turbomam Dec 3, 2024 •
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I forgot to escape the square brackets around FOODON with backslashes \[F... etc

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Copilot AI Mar 11, 2026

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This regex is effectively satisfied by any string that ends with a bracketed FOODON ID, even if earlier semicolon-separated terms don't have their own IDs (e.g., term1; term2 [FOODON:...] would match). If the intent is to validate a list of HACCP terms, each entry should include its own termLabel [FOODON:digits] (and if you keep ; as the separator, the repeating group should include the label as well). Tightening the pattern to require the termLabel + [FOODON:id] structure per item will prevent partially-specified multi-term values from being accepted.

Suggested change
pattern: ^.+\s*\[FOODON:\d+\](;\s*\[FOODON:\d+\])*$
pattern: ^[^;]+\s*\[FOODON:\d+\](;\s*[^;]+\s*\[FOODON:\d+\])*$

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structured_pattern:
syntax: ^{termLabel} \[{termID}\]$
interpolated: true
Expand Down Expand Up @@ -3741,8 +3742,7 @@ slots:
abs_air_humidity:
annotations:
Preferred_unit: gram per gram, kilogram per kilogram, kilogram, pound
description: Actual mass of water vapor - mh20 - present in the air water vapor
mixture
description: Actual mass of water vapor - mh20 - present in the air water vapor mixture
title: absolute air humidity
examples:
- value: 9 gram per gram
Expand Down Expand Up @@ -3793,8 +3793,7 @@ slots:
slot_uri: MIXS:0001009
required: true
additional_info:
description: Information that doesn't fit anywhere else. Can also be used to propose
new entries for fields with controlled vocabulary
description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary
title: additional info
keywords:
- information
Expand All @@ -3808,8 +3807,7 @@ slots:
string_serialization: '{integer}{text}'
slot_uri: MIXS:0000218
adj_room:
description: List of rooms (room number, room name) immediately adjacent to the
sampling room
description: List of rooms (room number, room name) immediately adjacent to the sampling room
title: adjacent rooms
keywords:
- adjacent
Expand All @@ -3824,10 +3822,7 @@ slots:
adjacent_environment:
annotations:
Expected_value: ENVO_01001110 or ENVO_00000070
description: Description of the environmental system or features that are adjacent
to the sampling site. This field accepts terms under ecosystem (http://purl.obolibrary.org/obo/ENVO_01001110)
and human construction (http://purl.obolibrary.org/obo/ENVO_00000070). Multiple
terms can be separated by pipes
description: Description of the environmental system or features that are adjacent to the sampling site. This field accepts terms under ecosystem (http://purl.obolibrary.org/obo/ENVO_01001110) and human construction (http://purl.obolibrary.org/obo/ENVO_00000070). Multiple terms can be separated by pipes
title: environment adjacent to site
examples:
- value: estuarine biome [ENVO:01000020]
Expand Down
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