Summarizing with LLMs
This notebook demonstrates how to summarize the output of LLMs using the datasette LLM command line tool.
See also:
Install the LLM command line tool
pip install llm
You may also want to install plugins for your models of choice:
pip install llm-deepseek
Summarize outputs
You can redirect any output you like to llm. For example, consider this OAK query to get definition of all kinds of hearts in Uberon:
[6]:
!runoak -i sqlite:obo:uberon definitions .sub "circulatory organ"
id label definition
UBERON:0000948 heart A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ.
UBERON:0007100 primary circulatory organ A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified].
UBERON:0015202 lymph heart A circulatory organ that is reponsible for pumping lymph throughout the body.
UBERON:0015227 peristaltic circulatory vessel A vessel down which passes a wave of muscular contraction, that forces the flow of haemolymphatic fluid.
UBERON:0015228 circulatory organ A hollow, muscular organ, which, by contracting rhythmically, contributes to the circulation of lymph, blood or analogs. Examples: a chambered vertebrate heart; the tubular peristaltic heart of ascidians; the dorsal vessel of an insect; the lymoh heart of a reptile.
UBERON:0015229 accessory circulatory organ A circulatory organ that is not responsible for primary circulation.
UBERON:0015230 dorsal vessel heart The caudal, pulsatile region of the dorsal vessel of the arthropod circulatory system.
UBERON:0034961 embryonic lymph heart A lymph heart that is part of an embryo.
UBERON:0034962 copulatory lymph heart A lymph heart that assists in the return of lymph from the penis to the venous system.
UBERON:0036259 cardial lymph propulsor A lymphatic propulsor that lies tightly against the truncus arteriosus, the major outflow tract of the amphibian heart.
UBERON:0034959 right lymph heart None
UBERON:0034960 left lymph heart None
[7]:
!runoak -i sqlite:obo:uberon definitions .sub "circulatory organ" | llm -m 4o -s "give a summary of these terms and critical comments on definitions"
This dataset contains definitions and critical comments on various anatomical terms related to circulatory and lymphatic organs. Here's a summary of the terms listed:
1. **Heart (UBERON:0000948):** Defined as a myogenic muscular organ in vertebrates, responsible for circulating blood through its chambers of cardiac muscle. It is characterized as the primary circulatory organ.
2. **Primary Circulatory Organ (UBERON:0007100):** Described as a hollow, muscular organ that rhythmically contracts to maintain blood circulation. This definition emphasizes the functional role of the heart or equivalent structures in different organisms.
. **Lymph Heart (UBERON:0015202):** A type of circulatory organ whose main function is to pump lymph throughout the body, highlighting its role in the lymphatic system rather than the blood circulatory system.
4. **Peristaltic Circulatory Vessel (UBERON:0015227):** A vessel that uses waves of muscular contraction to move haemolymphatic fluid, commonly found in invertebrates.
5. **Circulatory Organ (UBERON:0015228):** Describes a general category of muscle-based organs that contribute to the circulation of lymph, blood, or analogous fluids. Examples cover a range of biological structures beyond vertebrate hearts, such as insect dorsal vessels and reptilian lymph hearts.
. **Accessory Circulatory Organ (UBERON:0015229):** Defined as any circulatory organ that does not play a central role in primary circulation, indicating auxiliary support components within circulatory systems.
. **Dorsal Vessel Heart (UBERON:0015230):** This is explained as the pulsatile section of an arthropod's dorsal vessel, emphasizing its role within the insect circulatory system.
8. **Embryonic Lymph Heart (UBERON:0034961):** A lymph heart that functions within an embryo, which likely plays a role in early circulatory system development.
9. **Copulatory Lymph Heart (UBERON:0034962):** This organ assists in returning lymph from the penis to the venous system, underlining a specific physiological function.
10. **Cardial Lymph Propulsor (UBERON:0036259):** Located against the truncus arteriosus in amphibians, it functions in conjunction with the main outflow tract of the heart.
11. **Right Lymph Heart (UBERON:0034959) & Left Lymph Heart (UBERON:0034960):** These entries lack definitions, suggesting areas where further information and research are needed.
**Critical Comments on Definitions:**
definitions provided in this dataset are generally concise and specify the structural and functional characteristics of each organ. However, some definitions could benefit from more context about their biological significance and differences across species. The absence of information for the "Right Lymph Heart" and "Left Lymph Heart" suggests that these terms might either be very specific anatomical components not yet well-characterized, or they may need further clarification and research to accurately define their roles and significance within the biological taxonomy provided by UBERON.
Templates
The llm tool allows you to define templates.
llm templates edit summarize-definitions
Then in your editor:
system: give a summary of these terms and critical comments on definitions
[8]:
!runoak -i sqlite:obo:uberon definitions .sub "circulatory organ" | llm -m 4o -t summarize-definitions
This dataset provides definitions for various anatomical terms related to circulatory organs across different species, especially focusing on aspects of their structure and functions.
**Heart (UBERON:0000948)**: Defined as a myogenic muscular organ in vertebrates responsible for circulating blood, it's depicted as the primary organ in the cardiovascular system. Critical insight could involve the need for clarification on variations in structure and function across different vertebrate species.
2. **Primary Circulatory Organ (UBERON:0007100)**: Essentially an organ responsible for keeping blood or similar substances circulating via rhythmic contractions. The definition emphasizes its hollow and muscular nature. Critiques might focus on the broad definition that necessitates specifying how it differs from accessory organs in terms of function.
3. **Lymph Heart (UBERON:0015202)**: A specialized organ pumping lymph, reflecting its distinct role from blood-circulating hearts. The definition broadly indicates its role but leaves out specific biological distinctions that might benefit more from context about lymphatic roles and species specifics.
4. **Peristaltic Circulatory Vessel (UBERON:0015227)**: Characterized by its peristalsis-driven movement of haemolymphatic fluid, typical in certain invertebrates. Critical comments could address potential confusion with non-circulatory peristaltic functions and necessitate additional context on organism diversity.
**Circulatory Organ (UBERON:0015228)**: A broader category encompassing organs that use rhythmic contractions to aid circulation, including various heart types across species. This definition could be clearer with distinctions in organ origins (e.g., evolutionary paths) and functioning mechanisms.
. **Accessory Circulatory Organ (UBERON:0015229)**: These are defined as supportive rather than primary organs in aiding circulation. Critical comments may suggest defining criteria for what constitutes "accessory" and potential overlap with primary functions in certain conditions.
. **Dorsal Vessel Heart (UBERON:0015230)**: Specific to arthropods, it describes the pulsatile nature of their dorsal vessel system. Insights could focus on comparing this with vertebrate systems and clarifying its unique contributions to arthropod physiology.
. **Embryonic Lymph Heart (UBERON:0034961)**: This represents a lymph heart in an embryonic stage, underscoring developmental stages in lymphatic systems. Further definition could include comparative development timing across species.
. **Copulatory Lymph Heart (UBERON:0034962)**: Highlights a role in returning lymph from the penis to the venous system, particularly in reproductive context. Critical engagement might probe its existence across species and correlation to reproductive strategies.
. **Cardial Lymph Propulsor (UBERON:0036259)**: Applies to amphibians, lying against the truncus arteriosus, emphasizing a distinct lymphatic role. Definitions could improve by providing more detail on its structural uniqueness and interaction with other circulatory elements.
. **Right/Left Lymph Heart (UBERON:0034959 and UBERON:0034960)**: Currently lack definitions, necessitating clarification or investigation into whether these terms need unique definitions or if they are context-specific adaptations or roles.
Overall, while the dataset adequately defines the basic function and category of each term, critical comments might emphasize the need to offer more biological diversity context, specify differences between analogous structures across species, and clarify evolutionary or developmental stages mentioned but not detailed.
Gene summaries
Create a template for summarizing gene annotations:
llm templates edit summarize-gaf-for-gene
system: I will provide you with GAF for a gene. Summarize the function of the gene.
Give a one short description a biologist would understand.
You may weave together multiple terms where there is redundancy.
You should aim to be faithful to the GAF, but be aware that mistakes and over-annotation happens.
If you see things that are unlikely, you can omit these.
You may also produce some commentary at the end
(e.g. 'the GAF showed annotation to X but this contradicts what is known about the gene')
Do not focus on the evidence, or names, or IDs, or metadata about the annotation,
just write the biological narrative.
The exception is if this is really relevant (e.g. you may call into question a very old annotation if it
does not make sense).
Be aware that historically there has been over-annotation with experimental codes, for example, phenotypes from downstream effects.
These are less relevant, and you should focus on the core activity, cellular process, and localization.
You may however choose to briefly summarize phenotypic annotations (e.g. the role of G in process P has downstream effects E1, ...).
Use your judgment to explain the story biologically rather than simply regurgitating terms.
Note that the IBA code (inferred from biological ancestor) reflects high quality annotations in many species because these terms
have been reviewed in a phylogenetic context and checked for over-annotation.
But note that IBAs may sometimes be less complete, especially for organism-specific knowledge.
Use your own biological knowledge.
If aspects of the model are not clear, or you think there are errors, then at the end of your summary report on problems or anything that was not clear.
[9]:
!runoak -i amigo:NCBITaxon:9606 associations -p i,p -H --expand GO:0009229
# Query IDs: GO:0009229
# Ontology closure predicates: rdfs:subClassOf, BFO:0000050
#
# The results include a round of expansion
#
subject predicate object property_values subject_label predicate_label object_label negated publications evidence_type supporting_objects primary_knowledge_source aggregator_knowledge_source subject_closure subject_closure_label object_closure object_closure_label comments
UniProtKB:Q9BZV2 biolink:related_to GO:0009229 SLC19A3 None thiamine diphosphate biosynthetic process False GO_REF:0000107 IEA Ensembl infores:go
UniProtKB:Q9H3S4 biolink:related_to GO:0009229 TPK1 None thiamine diphosphate biosynthetic process False GO_REF:0000041 IEA UniProt infores:go
UniProtKB:Q9H3S4 biolink:related_to GO:0009229 TPK1 None thiamine diphosphate biosynthetic process False PMID:11342111 IDA UniProt infores:go
UniProtKB:Q9H3S4 biolink:related_to GO:0009229 TPK1 None thiamine diphosphate biosynthetic process False PMID:38547260 IDA UniProt infores:go
UniProtKB:Q9H3S4 biolink:related_to GO:0009229 TPK1 None thiamine diphosphate biosynthetic process False GO_REF:0000033 IBA GO_Central infores:go
UniProtKB:Q9HC21 biolink:related_to GO:0009229 SLC25A19 None thiamine diphosphate biosynthetic process False GO_REF:0000107 IEA Ensembl infores:go
UniProtKB:O60779 biolink:related_to GO:0009229 SLC19A2 None thiamine diphosphate biosynthetic process False GO_REF:0000107 IEA Ensembl infores:go
UniProtKB:Q9BU02 biolink:related_to GO:0009229 THTPA None thiamine diphosphate biosynthetic process False GO_REF:0000107 IEA Ensembl infores:go
UniProtKB:Q9BZV2 biolink:related_to GO:0005515 SLC19A3 None protein binding False PMID:32296183 IPI IntAct infores:go
UniProtKB:Q9BZV2 biolink:related_to GO:0005515 SLC19A3 None protein binding False PMID:32296183 IPI IntAct infores:go
UniProtKB:Q9BZV2 biolink:related_to GO:0005515 SLC19A3 None protein binding False PMID:32296183 IPI IntAct infores:go
UniProtKB:Q9BZV2 biolink:related_to GO:0005515 SLC19A3 None protein binding False PMID:32296183 IPI IntAct infores:go
UniProtKB:Q9BZV2 biolink:related_to GO:0005515 SLC19A3 None protein binding False PMID:32296183 IPI IntAct infores:go
UniProtKB:Q9BZV2 biolink:related_to GO:0005515 SLC19A3 None protein binding False PMID:32296183 IPI IntAct infores:go
UniProtKB:Q9BZV2 biolink:related_to GO:0005515 SLC19A3 None protein binding False PMID:32296183 IPI IntAct infores:go
UniProtKB:Q9BZV2 biolink:related_to GO:0005515 SLC19A3 None protein binding False PMID:32296183 IPI IntAct infores:go
UniProtKB:Q9BZV2 biolink:related_to GO:0005515 SLC19A3 None protein binding False PMID:32296183 IPI IntAct infores:go
UniProtKB:Q9BZV2 biolink:related_to GO:0005515 SLC19A3 None protein binding False PMID:32296183 IPI IntAct infores:go
UniProtKB:Q9BZV2 biolink:related_to GO:0005515 SLC19A3 None protein binding False PMID:32296183 IPI IntAct infores:go
UniProtKB:Q9BZV2 biolink:related_to GO:0015234 SLC19A3 None thiamine transmembrane transporter activity False GO_REF:0000024 ISS BHF-UCL infores:go
UniProtKB:Q9BZV2 biolink:related_to GO:0015234 SLC19A3 None thiamine transmembrane transporter activity False Reactome:R-HSA-199626 TAS Reactome infores:go
UniProtKB:Q9BZV2 biolink:related_to GO:0009229 SLC19A3 None thiamine diphosphate biosynthetic process False GO_REF:0000107 IEA Ensembl infores:go
UniProtKB:Q9BZV2 biolink:related_to GO:0015888 SLC19A3 None thiamine transport False PMID:11731220 IDA UniProt infores:go
UniProtKB:Q9BZV2 biolink:related_to GO:0015888 SLC19A3 None thiamine transport False PMID:33008889 IDA UniProt infores:go
UniProtKB:Q9BZV2 biolink:related_to GO:0015888 SLC19A3 None thiamine transport False PMID:35512554 IDA UniProt infores:go
UniProtKB:Q9BZV2 biolink:related_to GO:0015888 SLC19A3 None thiamine transport False PMID:35724964 IMP UniProt infores:go
UniProtKB:Q9BZV2 biolink:related_to GO:0031923 SLC19A3 None pyridoxine transport False PMID:33008889 IDA UniProt infores:go
UniProtKB:Q9BZV2 biolink:related_to GO:0031923 SLC19A3 None pyridoxine transport False PMID:35512554 IDA UniProt infores:go
UniProtKB:Q9BZV2 biolink:related_to GO:0031923 SLC19A3 None pyridoxine transport False PMID:35724964 IMP UniProt infores:go
UniProtKB:Q9BZV2 biolink:related_to GO:0031923 SLC19A3 None pyridoxine transport False PMID:36456177 IDA UniProt infores:go
UniProtKB:Q9BZV2 biolink:related_to GO:0042723 SLC19A3 None thiamine-containing compound metabolic process False Reactome:R-HSA-196819 TAS Reactome infores:go
UniProtKB:Q9BZV2 biolink:related_to GO:0071934 SLC19A3 None thiamine transmembrane transport False GO_REF:0000024 ISS BHF-UCL infores:go
UniProtKB:Q9BZV2 biolink:related_to GO:0005886 SLC19A3 None plasma membrane False Reactome:R-HSA-199626 TAS Reactome infores:go
UniProtKB:Q9BZV2 biolink:related_to GO:0016020 SLC19A3 None membrane False PMID:11136550 NAS UniProt infores:go
UniProtKB:Q9BZV2 biolink:related_to GO:0005886 SLC19A3 None plasma membrane False GO_REF:0000033 IBA GO_Central infores:go
UniProtKB:Q9BZV2 biolink:related_to GO:0055085 SLC19A3 None transmembrane transport False GO_REF:0000033 IBA GO_Central infores:go
UniProtKB:Q9BZV2 biolink:related_to GO:0015234 SLC19A3 None thiamine transmembrane transporter activity False GO_REF:0000033 IBA GO_Central infores:go
UniProtKB:Q9H3S4 biolink:related_to GO:0004788 TPK1 None thiamine diphosphokinase activity False PMID:11342111 IDA UniProt infores:go
UniProtKB:Q9H3S4 biolink:related_to GO:0004788 TPK1 None thiamine diphosphokinase activity False PMID:38547260 IDA UniProt infores:go
UniProtKB:Q9H3S4 biolink:related_to GO:0005515 TPK1 None protein binding False PMID:32296183 IPI IntAct infores:go
UniProtKB:Q9H3S4 biolink:related_to GO:0005524 TPK1 None ATP binding False GO_REF:0000043 IEA UniProt infores:go
UniProtKB:Q9H3S4 biolink:related_to GO:0016301 TPK1 None kinase activity False GO_REF:0000043 IEA UniProt infores:go
UniProtKB:Q9H3S4 biolink:related_to GO:0030975 TPK1 None thiamine binding False GO_REF:0000002 IEA InterPro infores:go
UniProtKB:Q9H3S4 biolink:related_to GO:0042802 TPK1 None identical protein binding False PMID:25502805 IPI IntAct infores:go
UniProtKB:Q9H3S4 biolink:related_to GO:0042802 TPK1 None identical protein binding False PMID:29892012 IPI IntAct infores:go
UniProtKB:Q9H3S4 biolink:related_to GO:0042802 TPK1 None identical protein binding False PMID:31515488 IPI IntAct infores:go
UniProtKB:Q9H3S4 biolink:related_to GO:0042802 TPK1 None identical protein binding False PMID:32296183 IPI IntAct infores:go
UniProtKB:Q9H3S4 biolink:related_to GO:0141200 TPK1 None UTP thiamine diphosphokinase activity False PMID:38547260 IDA UniProt infores:go
UniProtKB:Q9H3S4 biolink:related_to GO:0006772 TPK1 None thiamine metabolic process False GO_REF:0000107 IEA Ensembl infores:go
UniProtKB:Q9H3S4 biolink:related_to GO:0009229 TPK1 None thiamine diphosphate biosynthetic process False GO_REF:0000041 IEA UniProt infores:go
UniProtKB:Q9H3S4 biolink:related_to GO:0009229 TPK1 None thiamine diphosphate biosynthetic process False PMID:11342111 IDA UniProt infores:go
UniProtKB:Q9H3S4 biolink:related_to GO:0009229 TPK1 None thiamine diphosphate biosynthetic process False PMID:38547260 IDA UniProt infores:go
UniProtKB:Q9H3S4 biolink:related_to GO:0010510 TPK1 None regulation of acetyl-CoA biosynthetic process from pyruvate False PMID:38547260 IMP UniProt infores:go
UniProtKB:Q9H3S4 biolink:related_to GO:0005829 TPK1 None cytosol False Reactome:R-HSA-196761 TAS Reactome infores:go
UniProtKB:Q9H3S4 biolink:related_to GO:0004788 TPK1 None thiamine diphosphokinase activity False GO_REF:0000033 IBA GO_Central infores:go
UniProtKB:Q9H3S4 biolink:related_to GO:0009229 TPK1 None thiamine diphosphate biosynthetic process False GO_REF:0000033 IBA GO_Central infores:go
UniProtKB:Q9HC21 biolink:not GO:0030233 SLC25A19 None deoxynucleotide transmembrane transporter activity True PMID:15539640 IDA UniProt infores:go
UniProtKB:Q9HC21 biolink:not GO:0030233 SLC25A19 None deoxynucleotide transmembrane transporter activity True PMID:17035501 IDA UniProt infores:go
UniProtKB:Q9HC21 biolink:not GO:0030302 SLC25A19 None deoxynucleotide transport True PMID:15539640 IDA UniProt infores:go
UniProtKB:Q9HC21 biolink:related_to GO:0015297 SLC25A19 None antiporter activity False GO_REF:0000043 IEA UniProt infores:go
UniProtKB:Q9HC21 biolink:related_to GO:0030233 SLC25A19 None deoxynucleotide transmembrane transporter activity False PMID:11226231 TAS UniProt infores:go
UniProtKB:Q9HC21 biolink:related_to GO:0090422 SLC25A19 None thiamine pyrophosphate transmembrane transporter activity False PMID:17035501 IDA UniProt infores:go
UniProtKB:Q9HC21 biolink:related_to GO:0090422 SLC25A19 None thiamine pyrophosphate transmembrane transporter activity False Reactome:R-HSA-8875838 TAS Reactome infores:go
UniProtKB:Q9HC21 biolink:related_to GO:0009229 SLC25A19 None thiamine diphosphate biosynthetic process False GO_REF:0000107 IEA Ensembl infores:go
UniProtKB:Q9HC21 biolink:related_to GO:0030302 SLC25A19 None deoxynucleotide transport False PMID:11226231 NAS UniProt infores:go
UniProtKB:Q9HC21 biolink:related_to GO:0030974 SLC25A19 None thiamine pyrophosphate transmembrane transport False PMID:17035501 IDA UniProt infores:go
UniProtKB:Q9HC21 biolink:related_to GO:0042723 SLC25A19 None thiamine-containing compound metabolic process False Reactome:R-HSA-196819 TAS Reactome infores:go
UniProtKB:Q9HC21 biolink:related_to GO:0005634 SLC25A19 None nucleus False PMID:21630459 HDA UniProt infores:go
UniProtKB:Q9HC21 biolink:related_to GO:0005739 SLC25A19 None mitochondrion False GO_REF:0000052 IDA HPA infores:go
UniProtKB:Q9HC21 biolink:related_to GO:0005739 SLC25A19 None mitochondrion False GO_REF:0000052 IDA HPA infores:go
UniProtKB:Q9HC21 biolink:related_to GO:0005739 SLC25A19 None mitochondrion False GO_REF:0000052 IDA HPA infores:go
UniProtKB:Q9HC21 biolink:related_to GO:0005739 SLC25A19 None mitochondrion False PMID:15539640 IDA UniProt infores:go
UniProtKB:Q9HC21 biolink:related_to GO:0005739 SLC25A19 None mitochondrion False PMID:31506564 IDA UniProt infores:go
UniProtKB:Q9HC21 biolink:related_to GO:0005739 SLC25A19 None mitochondrion False PMID:34800366 HTP FlyBase infores:go
UniProtKB:Q9HC21 biolink:related_to GO:0005743 SLC25A19 None mitochondrial inner membrane False Reactome:R-HSA-8875838 TAS Reactome infores:go
UniProtKB:Q9HC21 biolink:related_to GO:0030974 SLC25A19 None thiamine pyrophosphate transmembrane transport False GO_REF:0000033 IBA GO_Central infores:go
UniProtKB:Q9HC21 biolink:related_to GO:0015234 SLC25A19 None thiamine transmembrane transporter activity False GO_REF:0000033 IBA GO_Central infores:go
UniProtKB:Q9HC21 biolink:related_to GO:0005743 SLC25A19 None mitochondrial inner membrane False GO_REF:0000033 IBA GO_Central infores:go
UniProtKB:O60779 biolink:related_to GO:0005515 SLC19A2 None protein binding False PMID:21836059 IPI UniProt infores:go
UniProtKB:O60779 biolink:related_to GO:0005515 SLC19A2 None protein binding False PMID:21836059 IPI IntAct infores:go
UniProtKB:O60779 biolink:related_to GO:0008517 SLC19A2 None folic acid transmembrane transporter activity False PMID:10542220 NAS UniProt infores:go
UniProtKB:O60779 biolink:related_to GO:0015234 SLC19A2 None thiamine transmembrane transporter activity False GO_REF:0000024 ISS BHF-UCL infores:go
UniProtKB:O60779 biolink:related_to GO:0015234 SLC19A2 None thiamine transmembrane transporter activity False PMID:10542220 TAS UniProt infores:go
UniProtKB:O60779 biolink:related_to GO:0015234 SLC19A2 None thiamine transmembrane transporter activity False PMID:21836059 IDA UniProt infores:go
UniProtKB:O60779 biolink:related_to GO:0015234 SLC19A2 None thiamine transmembrane transporter activity False Reactome:R-HSA-199626 TAS Reactome infores:go
UniProtKB:O60779 biolink:related_to GO:0007283 SLC19A2 None spermatogenesis False GO_REF:0000107 IEA Ensembl infores:go
UniProtKB:O60779 biolink:related_to GO:0009229 SLC19A2 None thiamine diphosphate biosynthetic process False GO_REF:0000107 IEA Ensembl infores:go
UniProtKB:O60779 biolink:related_to GO:0015884 SLC19A2 None folic acid transport False GO_REF:0000108 IEA GOC infores:go
UniProtKB:O60779 biolink:related_to GO:0015888 SLC19A2 None thiamine transport False PMID:10391222 IMP UniProt infores:go
UniProtKB:O60779 biolink:related_to GO:0015888 SLC19A2 None thiamine transport False PMID:10542220 IDA UniProt infores:go
UniProtKB:O60779 biolink:related_to GO:0015888 SLC19A2 None thiamine transport False PMID:10542220 NAS UniProt infores:go
UniProtKB:O60779 biolink:related_to GO:0015888 SLC19A2 None thiamine transport False PMID:33008889 IDA UniProt infores:go
UniProtKB:O60779 biolink:related_to GO:0015888 SLC19A2 None thiamine transport False PMID:35512554 IDA UniProt infores:go
UniProtKB:O60779 biolink:related_to GO:0015888 SLC19A2 None thiamine transport False PMID:35724964 IMP UniProt infores:go
UniProtKB:O60779 biolink:related_to GO:0031923 SLC19A2 None pyridoxine transport False PMID:33008889 IDA UniProt infores:go
UniProtKB:O60779 biolink:related_to GO:0031923 SLC19A2 None pyridoxine transport False PMID:35512554 IDA UniProt infores:go
UniProtKB:O60779 biolink:related_to GO:0042723 SLC19A2 None thiamine-containing compound metabolic process False Reactome:R-HSA-196819 TAS Reactome infores:go
UniProtKB:O60779 biolink:related_to GO:0071934 SLC19A2 None thiamine transmembrane transport False GO_REF:0000024 ISS BHF-UCL infores:go
UniProtKB:O60779 biolink:related_to GO:0005886 SLC19A2 None plasma membrane False PMID:21836059 IDA UniProt infores:go
UniProtKB:O60779 biolink:related_to GO:0005886 SLC19A2 None plasma membrane False Reactome:R-HSA-199626 TAS Reactome infores:go
UniProtKB:O60779 biolink:related_to GO:0016020 SLC19A2 None membrane False PMID:10542220 NAS UniProt infores:go
UniProtKB:O60779 biolink:related_to GO:0005886 SLC19A2 None plasma membrane False GO_REF:0000033 IBA GO_Central infores:go
UniProtKB:O60779 biolink:related_to GO:0015888 SLC19A2 None thiamine transport False GO_REF:0000033 IBA GO_Central infores:go
UniProtKB:O60779 biolink:related_to GO:0015234 SLC19A2 None thiamine transmembrane transporter activity False GO_REF:0000033 IBA GO_Central infores:go
UniProtKB:O60779 biolink:related_to GO:0055085 SLC19A2 None transmembrane transport False GO_REF:0000033 IBA GO_Central infores:go
UniProtKB:Q9BU02 biolink:related_to GO:0000287 THTPA None magnesium ion binding False GO_REF:0000024 ISS UniProt infores:go
UniProtKB:Q9BU02 biolink:related_to GO:0005515 THTPA None protein binding False PMID:32296183 IPI IntAct infores:go
UniProtKB:Q9BU02 biolink:related_to GO:0016787 THTPA None hydrolase activity False PMID:11827967 TAS UniProt infores:go
UniProtKB:Q9BU02 biolink:related_to GO:0050333 THTPA None thiamine triphosphate phosphatase activity False PMID:11827967 IDA UniProt infores:go
UniProtKB:Q9BU02 biolink:related_to GO:0006091 THTPA None generation of precursor metabolites and energy False PMID:11827967 NAS UniProt infores:go
UniProtKB:Q9BU02 biolink:related_to GO:0006772 THTPA None thiamine metabolic process False PMID:11827967 TAS UniProt infores:go
UniProtKB:Q9BU02 biolink:related_to GO:0009229 THTPA None thiamine diphosphate biosynthetic process False GO_REF:0000107 IEA Ensembl infores:go
UniProtKB:Q9BU02 biolink:related_to GO:0016311 THTPA None dephosphorylation False PMID:11827967 IDA UniProt infores:go
UniProtKB:Q9BU02 biolink:related_to GO:0042357 THTPA None thiamine diphosphate metabolic process False GO_REF:0000024 ISS UniProt infores:go
UniProtKB:Q9BU02 biolink:related_to GO:0005829 THTPA None cytosol False Reactome:R-HSA-965067 TAS Reactome infores:go
UniProtKB:Q9BU02 biolink:related_to GO:0000287 THTPA None magnesium ion binding False GO_REF:0000033 IBA GO_Central infores:go
UniProtKB:Q9BU02 biolink:related_to GO:0050333 THTPA None thiamine triphosphate phosphatase activity False GO_REF:0000033 IBA GO_Central infores:go
UniProtKB:Q9BU02 biolink:related_to GO:0042357 THTPA None thiamine diphosphate metabolic process False GO_REF:0000033 IBA GO_Central infores:go
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!runoak -i amigo:NCBITaxon:9606 associations -p i,p -H --expand GO:0009229 | llm -m 4o -t summarize-gaf-for-gene
The gene annotated with the process "thiamine diphosphate biosynthetic process" is involved in the synthesis of thiamine diphosphate (TDP), a coenzyme form of thiamine (vitamin B1) critical for various enzymatic reactions. Here's a summary of the functions of related gene products:
TPK1 (Thiamine Pyrophosphokinase 1)**: TPK1 plays a direct role in the thiamine diphosphate biosynthetic process by catalyzing the conversion of thiamine (vitamin B1) into thiamine diphosphate. This enzyme exhibits thiamine diphosphokinase activity, utilizing ATP in the phosphorylation process. It is also involved in the regulation of acetyl-CoA biosynthesis from pyruvate, a crucial step in energy metabolism. It predominantly localizes in the cytosol.
2. **SLC19A2 and SLC19A3 (Thiamine Transporters)**: These are integral membrane proteins that primarily facilitate the transmembrane transport of thiamine and its derivatives. They exhibit thiamine transmembrane transporter activity and localize to the plasma membrane. They also partake in transport processes of other vitamin B compounds, like pyridoxine. SLC19A2 is also implicated in folic acid transport and localized to the plasma membrane.
SLC25A19**: This gene encodes a transporter responsible for the transmembrane transport of thiamine pyrophosphate (TPP), particularly across the mitochondrial inner membrane. Although associated with thiamine diphosphate biosynthetic processes, it primarily functions as a thiamine pyrophosphate transmembrane transporter, ensuring TPP availability within mitochondria for enzymatic processes.
**THTPA (Thiamine Triphosphate Phosphatase)**: This enzyme is involved in the breakdown of thiamine triphosphate to thiamine diphosphate, contributing to the overall maintenance of thiamine phosphate balance within the cell. THTPA exhibits thiamine triphosphate phosphatase and general hydrolase activity with a prominent role in the cytosol.
these proteins coordinate in the transport, synthesis, and utilization of thiamine derivatives, ensuring the bioavailability of thiamine diphosphate for critical metabolic pathways.
**Commentary**: The annotations broadly reflect the core function of these genes in thiamine metabolism and transport. The GAF suggests some erroneous and overlapping annotations, such as the inclusion of folic acid transport for SLC19A2, which primarily functions as a thiamine transporter. Additionally, the "thiamine diphosphate biosynthetic process" might not directly apply to the transporters like SLC19A2 and SLC19A3, as these are more focused on the transport aspect rather than direct synthesis.
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