Support for human phenotype ontology (HPO)

[daboe01]

https://hpo.jax.org/browse/term/HP:0030534
i.e. mapping to these codes
HP:0030557
HP:0030559
HP:0030565
HP:0030555
HP:0030564
HP:0030567
HP:0030558
HP:0030563
HP:0030560
HP:0030556
HP:0030554
HP:0030561
HP:0030566
HP:0030568
HP:0030562
HP:0030534

[daboe01]

Hi Michael,

I would like to briefly explain the background of this suggestion.

The Human Phenotype Ontology (HPO) is an international standard for the structured description of clinical phenotypic abnormalities. It is widely used in international registries and clinical databases—particularly in the field of rare diseases—to make clinical data machine-readable and standardized across different platforms.

HPO also covers visual acuity. Under the parent term "Decreased visual acuity" (HP:0030534), there are specific sub-terms representing different ranges of visual impairment (e.g., mild, moderate, or severe visual impairment).

Since FrACT is frequently used in clinical and research settings to measure visual acuity, it would be highly beneficial if the tool could map the measured visual acuity (or logMAR score) to the corresponding HPO code and output it. This would facilitate the direct, standardized entry of test results into medical registries.

Thank you for considering this idea.

[michaelbach]

Thank you, Daniel, now I get it. Great idea! So I would output, e.g. HP:0030554 if the LogMAR value (rounded to 1 significant digit) were 0.1. Should this be on screen, or rather in the string that can be copied to the clipboard / read out via HTML messages? Or would it make sense to add an HTML message that can query the HP code?

[daboe01]

i would make this optional and would prefer the clipboard route.

[michaelbach]

ok, so i would add "… ⇥ HPOCode ⇥ HP:0030554" to this string?
BTW: If it's in the clipboard string, it is automatically also in the export data retrieved via HTML messages.

[daboe01]

IMHO you could omit "HPOcode ⇥" as this is redundant.

…

Am 18.07.2026 um 13:52 schrieb Michael Bach ***@***.***>: ok, so i would add "… ⇥ HPOcode ⇥ HP:0030554" to this string? BTW: If it's in the clipboard string, it is automatically also in the export data retrieved via HTML messages. — Reply to this email directly, view it on GitHub <#55?email_source=notifications&email_token=AABDXH3RINA7YUDIZJFSU6L5FNQH3A5CNFSNUABIM5UWIORPF5TWS5BNNB2WEL2ENFZWG5LTONUW63SDN5WW2ZLOOQXTCNZWHAYDKMBVUZZGKYLTN5XKMYLVORUG64VFMV3GK3TUVRTG633UMVZF6Y3MNFRWW#discussioncomment-17680505>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AABDXH75RZ23UF5VL5W57DD5FNQH3AVCNFSNUABIKJSXA33TNF2G64TZHMZDMNRWGAZDIOBSHNCGS43DOVZXG2LPNY5TCMBUGQ4DONZWUF3AE>. Triage notifications, keep track of coding agent tasks and review pull requests on the go with GitHub Mobile for iOS <https://github.com/notifications/mobile/ios/AABDXH4XWZTPDVE3M7UV3UD5FNQH3A5CNFSNUABIM5UWIORPF5TWS5BNNB2WEL2ENFZWG5LTONUW63SDN5WW2ZLOOQXTCNZWHAYDKMBVUZZGKYLTN5XKMYLVORUG64VFMV3GK3TUVJTG633UMVZF62LPOM> and Android <https://github.com/notifications/mobile/android/AABDXH4PVQKB6VFVDJKQ2XL5FNQH3A5CNFSNUABIM5UWIORPF5TWS5BNNB2WEL2ENFZWG5LTONUW63SDN5WW2ZLOOQXTCNZWHAYDKMBVUZZGKYLTN5XKMYLVORUG64VFMV3GK3TUVZTG633UMVZF6YLOMRZG62LE>. Download it today! You are receiving this because you authored the thread.

[michaelbach]

Yes, but then one could not parse it easily. All other output values are not positionally encoded, but in a "key ⇥ value ⇥" format.
Here
https://michaelbach.de/fract/FrACT10/readResultString.html
is a parsing example.

[michaelbach]

And more questions: if acuity is better (smaller) then 0.05 LogMAR, do I add nothing or is there a placeholder for "normal" acuity? BTW: 0.1 LogMAR would count as normal for me.

[daboe01]

i would use 0.1 LogMAR for normal

[michaelbach]

Exactly, but it's classified under "Abnormal best corrected visual acuity test" in HPO

[michaelbach]

Resolved with fd33237

In Settings>Acuity there is now (in the center) a checkbox "Export HBO code".