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CompBioBench item

ensembl-grab-q1

Question

Convert all of the following to Ensembl gene IDs. Provide the ID without the Ensembl version (e.g., ENSGXXXXXXXXXXXX not ENSGXXXXXXXXXXXX.XX). Respond with semi-colon separated values, no spaces. Inputs: 1. NM_001276266.2 2. TERB2 3. ENST00000267814 4. chr15:45167214-45187966 (hg38) 5. GeneID:9153 6. NP_922946.1 7. MIM:617658 8. BEN domain containing 5, transcript variant 6.

Predicted answer
ENSG00000140254;ENSG00000167014;ENSG00000140263;ENSG00000138606;ENSG00000137860;ENSG00000166920;ENSG00000137767;ENSG00000162373Most likely answer for this question; not uniquely determined from submitted scores.
Domain
Genomics
Question style
Retrieval

An answer can be uniquely inferred for 54 of 100 questions from submitted scores. Green: correct · Red: incorrect. For questions without a uniquely determined answer: Blue: matches prediction · Orange: differs from prediction. These are inferred answer checks, not official per-question grades.

Galaxy

12/12 terminal item results

UDT = user-defined tool: custom code executed by Galaxy. Route badges summarize analysis tools, excluding uploads and automatic conversions. How usage is counted.

Codex GPT-5.5

3 replicates
Codex GPT-5.5

Replicate 1

Matches predictionUDT-only
AnswerENSG00000140254;ENSG00000167014;ENSG00000140263;ENSG00000138606;ENSG00000137860;ENSG00000166920;ENSG00000137767;ENSG00000162373
Workflow
Gene ID crosswalk via public annotation APIsGene ID crosswalk acceptance check
Galaxy historyAgent trace
Codex GPT-5.5

Replicate 2

Matches predictionUDT-only
AnswerENSG00000140254;ENSG00000167014;ENSG00000140263;ENSG00000138606;ENSG00000137860;ENSG00000166920;ENSG00000137767;ENSG00000162373
Workflow
Ensembl ID MapperEnsembl ID Mapper v2Ensembl ID Mapper v3
Total tokens
2.1M
Output
32.2K
Galaxy historyAgent trace
Codex GPT-5.5

Replicate 3

Matches predictionStandard tools only
AnswerENSG00000140254;ENSG00000167014;ENSG00000140263;ENSG00000138606;ENSG00000137860;ENSG00000166920;ENSG00000137767;ENSG00000162373
Workflow
Galaxy dataset inspection
Total tokens
974.7K
Output
8.0K
Galaxy historyAgent trace

Codex GPT-5.6 Sol

3 replicates
Codex GPT-5.6 Sol

Replicate 1

Matches predictionUDT-only
AnswerENSG00000140254;ENSG00000167014;ENSG00000140263;ENSG00000138606;ENSG00000137860;ENSG00000166920;ENSG00000137767;ENSG00000162373
Workflow
Mixed identifier resolution probeMixed identifier resolution acceptance
Total tokens
547.9K
Output
6.8K
Galaxy historyAgent trace
Codex GPT-5.6 Sol

Replicate 2

Matches predictionUDT-only
AnswerENSG00000140254;ENSG00000167014;ENSG00000140263;ENSG00000138606;ENSG00000137860;ENSG00000166920;ENSG00000137767;ENSG00000162373
Workflow
Mixed identifier authoritative diagnosticMixed identifier exact narrowingFinal authoritative Ensembl gene IDs
Total tokens
812.9K
Output
10.9K
Galaxy historyAgent trace
Codex GPT-5.6 Sol

Replicate 3

Matches predictionUDT + standard tools
AnswerENSG00000140254;ENSG00000167014;ENSG00000140263;ENSG00000138606;ENSG00000137860;ENSG00000166920;ENSG00000137767;ENSG00000162373
Workflow
Gprofiler ConvertAuthoritative Ensembl Gene ID DiagnosticSummarize Authoritative Gene ID DiagnosticCompact Authoritative Gene ID EvidenceTargeted Coordinate and BEND5 Validation1 more tools
Total tokens
2.4M
Output
15.1K
Galaxy historyAgent trace

Codex + DeepSeek-v4-pro-0813

3 replicates
Codex + DeepSeek-v4-pro-0813

Replicate 1

Matches predictionStandard tools only
AnswerENSG00000140254;ENSG00000167014;ENSG00000140263;ENSG00000138606;ENSG00000137860;ENSG00000166920;ENSG00000137767;ENSG00000162373
Workflow
No Galaxy tool job recorded
Total tokens
10.8M
Output
41.6K
Galaxy historyAgent trace
Codex + DeepSeek-v4-pro-0813

Replicate 2

Matches predictionStandard tools only
AnswerENSG00000140254;ENSG00000167014;ENSG00000140263;ENSG00000138606;ENSG00000137860;ENSG00000166920;ENSG00000137767;ENSG00000162373
Workflow
AnnotatemyidsDatasets Download GeneGtftobed12Bedtools IntersectbedGtf Filter By Attribute Values List
Total tokens
5.6M
Output
30.4K
Galaxy historyAgent trace
Codex + DeepSeek-v4-pro-0813

Replicate 3

Matches predictionStandard tools only
AnswerENSG00000140254;ENSG00000167014;ENSG00000140263;ENSG00000138606;ENSG00000137860;ENSG00000166920;ENSG00000137767;ENSG00000162373
Workflow
Gprofiler ConvertDatasets Download Gene
Total tokens
2.6M
Output
18.6K
Galaxy historyAgent trace

Codex GPT-5.6 Luna

3 replicates
Codex GPT-5.6 Luna

Replicate 1

Matches predictionStandard tools only
AnswerENSG00000140254;ENSG00000167014;ENSG00000140263;ENSG00000138606;ENSG00000137860;ENSG00000166920;ENSG00000137767;ENSG00000162373
Workflow
AnnotatemyidsDatasets Download Gene
Total tokens
6.3M
Output
14.5K
Galaxy historyAgent trace
Codex GPT-5.6 Luna

Replicate 2

Matches predictionStandard tools only
AnswerENSG00000140254;ENSG00000167014;ENSG00000140263;ENSG00000138606;ENSG00000137860;ENSG00000166920;ENSG00000137767;ENSG00000162373
Workflow
AnnotatemyidsDatasets Download GeneNcbi Acc DownloadGprofiler Convert
Total tokens
8.2M
Output
24.6K
Galaxy historyAgent trace
Codex GPT-5.6 Luna

Replicate 3

Matches predictionStandard tools only
AnswerENSG00000140254;ENSG00000167014;ENSG00000140263;ENSG00000138606;ENSG00000137860;ENSG00000166920;ENSG00000137767;ENSG00000162373
Workflow
Datasets Download GeneAnnotatemyidsEbi Search Rest Results
Total tokens
7.6M
Output
29.2K
Galaxy historyAgent trace

Anycode

13/13 terminal item results

Codex GPT-5.5

3 replicates
Codex GPT-5.5

Replicate 1

Matches prediction
AnswerENSG00000140254;ENSG00000167014;ENSG00000140263;ENSG00000138606;ENSG00000137860;ENSG00000166920;ENSG00000137767;ENSG00000162373
Workflow
Local code
Agent trace
Codex GPT-5.5

Replicate 2

Matches prediction
AnswerENSG00000140254;ENSG00000167014;ENSG00000140263;ENSG00000138606;ENSG00000137860;ENSG00000166920;ENSG00000137767;ENSG00000162373
Workflow
Local code
Agent trace
Codex GPT-5.5

Replicate 3

Matches prediction
AnswerENSG00000140254;ENSG00000167014;ENSG00000140263;ENSG00000138606;ENSG00000137860;ENSG00000166920;ENSG00000137767;ENSG00000162373
Workflow
Local code
Agent trace

Codex GPT-5.6 Sol

3 replicates
Codex GPT-5.6 Sol

Replicate 1

Matches prediction
AnswerENSG00000140254;ENSG00000167014;ENSG00000140263;ENSG00000138606;ENSG00000137860;ENSG00000166920;ENSG00000137767;ENSG00000162373
Workflow
Local code
Agent trace
Codex GPT-5.6 Sol

Replicate 2

Matches prediction
AnswerENSG00000140254;ENSG00000167014;ENSG00000140263;ENSG00000138606;ENSG00000137860;ENSG00000166920;ENSG00000137767;ENSG00000162373
Workflow
Local codePython
Agent trace
Codex GPT-5.6 Sol

Replicate 3

Matches prediction
AnswerENSG00000140254;ENSG00000167014;ENSG00000140263;ENSG00000138606;ENSG00000137860;ENSG00000166920;ENSG00000137767;ENSG00000162373
Workflow
Local code
Agent trace

Codex + DeepSeek-v4-pro-0813

3 replicates
Codex + DeepSeek-v4-pro-0813

Replicate 1

Matches prediction
AnswerENSG00000140254;ENSG00000167014;ENSG00000140263;ENSG00000138606;ENSG00000137860;ENSG00000166920;ENSG00000137767;ENSG00000162373
Workflow
Local codePython
Total tokens
247.2K
Output
4.8K
Agent trace
Codex + DeepSeek-v4-pro-0813

Replicate 2

Matches prediction
AnswerENSG00000140254;ENSG00000167014;ENSG00000140263;ENSG00000138606;ENSG00000137860;ENSG00000166920;ENSG00000137767;ENSG00000162373
Workflow
Local codePython
Total tokens
942.4K
Output
10.3K
Agent trace
Codex + DeepSeek-v4-pro-0813

Replicate 3

Matches prediction
AnswerENSG00000140254;ENSG00000167014;ENSG00000140263;ENSG00000138606;ENSG00000137860;ENSG00000166920;ENSG00000137767;ENSG00000162373
Workflow
Local code
Total tokens
520.9K
Output
11.0K
Agent trace

Codex GPT-5.6 Luna

3 replicates
Codex GPT-5.6 Luna

Replicate 1

Matches prediction
AnswerENSG00000140254;ENSG00000167014;ENSG00000140263;ENSG00000138606;ENSG00000137860;ENSG00000166920;ENSG00000137767;ENSG00000162373
Workflow
Local code
Agent trace
Codex GPT-5.6 Luna

Replicate 2

Matches prediction
AnswerENSG00000140254;ENSG00000167014;ENSG00000140263;ENSG00000138606;ENSG00000137860;ENSG00000166920;ENSG00000137767;ENSG00000162373
Workflow
Local code
Agent trace
Codex GPT-5.6 Luna

Replicate 3

Matches prediction
AnswerENSG00000140254;ENSG00000167014;ENSG00000140263;ENSG00000138606;ENSG00000137860;ENSG00000166920;ENSG00000137767;ENSG00000162373
Workflow
Local code
Agent trace

Codex GPT-6 Astra

1 replicate
Codex GPT-6 Astra

Replicate 1

Matches prediction
AnswerENSG00000140254;ENSG00000167014;ENSG00000140263;ENSG00000138606;ENSG00000137860;ENSG00000166920;ENSG00000137767;ENSG00000162373
Workflow
Local codePython
Total tokens
69.3K
Output
810
Agent trace