Hacktoberfest 2026: le issue che i maintainer hanno segnato per ottobre, aperte e adatte ai principianti. Sfoglia le issue Hacktoberfest

v2: Combining experiment and condition tables

Aperta
  • Qualcosa non va?
#657 1 commento 0 reazioni 0 assegnatari Vedi su GitHub

Nessuno ha ancora preso questa issue.

Valutazione

Difficoltà
5/5
Tempo stimato
Più di una settimana
Idoneità per principianti
25/100
Tipo di issue
Funzionalità
Chiarezza
Da chiarire
Stato di attività
Ferma
Ambito
bioinformatics

Direzione di ricerca

Start by reviewing the current v2 condition table and experiment table definitions described in the issue, then compare them with the proposed long experiment-table examples. Resolve whether conditionId can be removed and how timed target changes should be represented. Done means the schema decision is agreed and its implications for existing v2 data are documented.

Scritto dal modello di indicizzazione a partire dal testo della issue.

Descrizione

Problem: The current condition table only allows entry of the conditionId, targetId and targetValue. In v1, multiple targets could be specified for each condition. This allowed description of a whole experiment in one line, but the changes had to occur at time = 0.

v2 allows different conditions to occur at different times. This is an improvement as this reflects experimental protocols better. It also allows introduction of a 'forcing function' of sorts with stepwise changes in the parameters.

I propose that the change from wide condition tables to long condition tables obviates the need for the condition table and experiment tables should have the following columns:
experimentId, time, targetId, targetValue

Example:
v1 Alkan_SciSig2018 condition table (first two entries):
conditionId | Dox_level | Gem_level | SN38_level
model1_data1 | 0.0 | 0.0 | 0.0
model1_data2 | 0.0 | 0.0003 | 0.0

v2 Alkan_SciSig2018 condition table:
conditionId | targatID | targetValue
model1_data1 | Dox_level | 0.0
model1_data1 | Gem_level | 0.0
model1_data1 | SN38_level| 0.0
model1_data2 | Dox_level | 0.0
model1_data2 | Gem_level | 0.0003
model1_data2 | SN38_level| 0.0

v2 Alkan_SciSig2018 experiment table:
experimentId | time | conditionId
experiment1 | 0 | model1_data1
experiment2 | 0 | model1_data2

Proposed v2 Alkan_SciSig2018 experiment table:
experimentId | time | targatID | targetValue
experiment1 | 0 | Dox_level | 0.0
experiment1 | 0 | Gem_level | 0.0
experiment1 | 0 | SN38_level| 0.0
experiment2 | 0 | Dox_level | 0.0
experiment2 | 0 | Gem_level | 0.0003
experiment2 | 0 | SN38_level| 0.0

If, for example, experiment2 was a pulse of Gem_level, then it would be:
experimentId | time | targatID | targetValue
experiment1 | 0 | Dox_level | 0.0
experiment1 | 0 | Gem_level | 0.0
experiment1 | 0 | SN38_level| 0.0
experiment2 | 0 | Dox_level | 0.0
experiment2 | 0 | Gem_level | 0.0003
experiment2 | 10 | Gem_level | 0.0
experiment2 | 0 | SN38_level| 0.0

The current equivalent would be:
v2 Alkan_SciSig2018 experiment table:
experimentId | time | conditionId
experiment1 | 0 | model1_data1
experiment2 | 0 | model1_data2
experiment2 | 10 | model1_data1

which would introduce two unneeded events or a new condition. Because the conditionId is used nowhere else besides the experiment table, you will be creating a bunch of conditionIds for minor benefits. I agree that the benefits would be greater if the condition table was still wide.

Lingua principale
Nessun dato sulla lingua
Stelle
67
Fork
16
Merge medio
1g 19h
PR unite (30g)
1

Preparare l'ambiente

Come iniziare

  1. Leggi tutta la issue e poi la guida ai contributi del progetto.
  2. Commenta sulla issue per dire che te ne occupi tu — evita che due persone facciano lo stesso lavoro.
  3. Fai un fork del repository e lavora su un branch.
  4. Apri una pull request che faccia riferimento al numero della issue.

Altre issue di PEtab-dev/PEtab

Tutte le issue di PEtab-dev/PEtab

Issue simili

Altre issue su Bioinformatics

Ricevi le nuove issue nella tua casella

Un breve riepilogo di issue GitHub adatte ai principianti.