Summarizing with LLMs
This notebook demonstrates how to summarize the output of LLMs using the datasette LLM command line tool.
See also:
[How to use LLMs with OAK](https://incatools.github.io/ontology-access-kit/howtos/use-llms.html
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:
[1]:
!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
[2]:
!runoak -i sqlite:obo:uberon definitions .sub "circulatory organ" | llm -m 4o -s "give a summary of these terms and critical comments on definitions"
The terms provided mainly describe various structures within the circulatory system, both in vertebrates and invertebrates, with a focus on definitions from anatomical and biological perspectives. Here is a summary of the terms along with critical comments on their definitions:
1. **Heart (UBERON:0000948):** Defined as a myogenic muscular organ in vertebrates, responsible for circulating blood through cardiac muscle chambers. The term appropriately highlights the heart’s primary function and structural characteristics.
2. **Primary Circulatory Organ (UBERON:0007100):** Described as a hollow, muscular organ that maintains blood circulation through rhythmic contractions. The definition is clear, albeit a bit redundant with the general concept of a "heart."
3. **Lymph Heart (UBERON:0015202):** Defined as an organ pumping lymph throughout the body. The definition clearly states its function, but it might benefit from specifying its presence in particular animal groups.
4. **Peristaltic Circulatory Vessel (UBERON:0015227):** A vessel where muscular contractions propel fluid, specifically haemolymph. The definition is clear, but could use more context or examples of organisms in which such structures are found.
5. **Circulatory Organ (UBERON:0015228):** Broadly covers any hollow, muscular organ aiding blood, lymph, or fluid circulation. The examples provided enhance understanding, though the broad nature of the definition might necessitate more clarity or distinction between types.
6. **Accessory Circulatory Organ (UBERON:0015229):** An organ not primarily responsible for circulation, suggesting a supportive role. This generally makes sense, but would benefit from specific examples for clarity.
7. **Dorsal Vessel Heart (UBERON:0015230):** Describes the pulsatile region of the arthropod dorsal vessel, indicating its role in the circulatory system. The definition is precise for those familiar with arthropod anatomy but could confuse those without such background.
8. **Embryonic Lymph Heart (UBERON:0034961):** Specifies a lymph heart within an embryo. This is straightforward, however, further description of its role during development could enhance understanding.
9. **Copulatory Lymph Heart (UBERON:0034962):** Involves lymph return from the penis to the venous system. The definition is clear, yet specialized, relevant mostly to anatomy involving reproductive systems.
10. **Cardial Lymph Propulsor (UBERON:0036259):** A lymph structure associated with the amphibian heart’s major outflow tract. The definition is precise for specific studies of amphibian physiology.
11. **Right Lymph Heart (UBERON:0034959) & Left Lymph Heart (UBERON:0034960):** These terms lack definitions, which raises questions about their specific roles and anatomical details; adding definitions would improve completeness and understanding.
Critical observations indicate that many definitions would benefit from contextual enlargement or specification of their presence and role in different species, enhancing educational value. Furthermore, terms without definitions need elaboration for comprehensive utility.
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
[3]:
!runoak -i sqlite:obo:uberon definitions .sub "circulatory organ" | llm -m 4o -t summarize-definitions
The dataset provides definitions for various types of circulatory organs and structures within the UBERON ontology, which is a comprehensive multi-species anatomy ontology encompassing multiple biological domains. Here is a summary of each term included:
1. **Heart (UBERON:0000948)**: Described as a myogenic muscular organ within the vertebrate cardiovascular system. It is the primary circulatory organ that functions by moving blood throughout the body via chambers of cardiac muscle.
2. **Primary Circulatory Organ (UBERON:0007100)**: A hollow, muscular organ that maintains blood circulation through rhythmic contractions. The definition is adapted from the Gene Ontology (GO).
3. **Lymph Heart (UBERON:0015202)**: A circulatory organ tasked with pumping lymphatic fluid throughout the body. It serves a function analogous to the heart but specific to lymph circulation.
4. **Peristaltic Circulatory Vessel (UBERON:0015227)**: Described as a vessel in which muscular contractions send waves that propel haemolymphatic fluid forward, common in certain invertebrates.
5. **Circulatory Organ (UBERON:0015228)**: This broader category includes any hollow, muscular organ that contributes to the circulation of blood, lymph, or their analogs. Examples include the vertebrate heart, ascidian peristaltic heart, the insect dorsal vessel, and a reptile's lymph heart.
6. **Accessory Circulatory Organ (UBERON:0015229)**: Any circulatory organ that does not play the primary role in circulation, implying a supportive or secondary role.
7. **Dorsal Vessel Heart (UBERON:0015230)**: A section of the dorsal vessel in arthropods, it is characterized as pulsatile, assisting in their circulatory system.
8. **Embryonic Lymph Heart (UBERON:0034961)**: A lymph heart that is active during the embryonic stage of development.
9. **Copulatory Lymph Heart (UBERON:0034962)**: A specialized lymph heart aiding in returning lymph from the penis to the venous system.
10. **Cardial Lymph Propulsor (UBERON:0036259)**: Positioned closely against the truncus arteriosus in amphibians, it helps propel lymphatic fluid, acting near the heart's outflow tract.
11. **Right Lymph Heart (UBERON:0034959)** and **Left Lymph Heart (UBERON:0034960)**: These entries lack defined descriptions in the dataset, suggesting they might represent specific anatomical structures known in certain species but not yet fully characterized in this context.
**Critical Comments on Definitions:**
- **Incompleteness and Specificity:** Some entries, like the right and left lymph heart, are missing definitions, which indicate a need for further research or input in these areas. Definitions should be expanded to clarify their unique roles or confirm their existence in various species.
- **Overlap and Clarity:** There is potential overlap in the definitions of terms like "circulatory organ" and "primary circulatory organ," which might cause confusion regarding their distinct functionalities and hierarchies. It would be beneficial to delineate these more clearly within the ontology.
- **Use of Examples and Context:** The use of examples, such as the mention of ascidians and insects in the circulatory organ definition, enriches understanding but might require caveats for context-specific interpretations.
Overall, while the given definitions are fairly descriptive of the various components of circulatory systems across different organisms, further refinement and detail, particularly where missing or vague, could improve comprehensiveness and usability in biological research and applications.
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.
[8]:
!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 products associated with the thiamine diphosphate biosynthetic process (GO:0009229) involve several proteins including SLC19A3, TPK1, SLC25A19, SLC19A2, and THTPA, each contributing to the synthesis and transport of thiamine-related compounds in different capacities.
SLC19A3 is primarily involved in the transport of thiamine and pyridoxine across the plasma membrane, displaying thiamine transmembrane transporter activity. It facilitates thiamine transmembrane transport and is located on the plasma membrane. This protein also plays a role in thiamine transport in general, contributing to the overall metabolic process of thiamine-containing compounds.
TPK1 (thiamine pyrophosphate kinase) catalyzes the ATP-dependent phosphorylation of thiamine to form thiamine diphosphate, which is the active form of thiamine used as a coenzyme in various enzymatic reactions. It has been detected in the cytosol and also possesses kinase and ATP binding activity.
SLC25A19 is responsible for the transmembrane transport of thiamine pyrophosphate into mitochondria. It shows activity as a thiamine pyrophosphate transmembrane transporter, indicating its critical role in mitochondrial functions related to thiamine metabolism. This protein is associated with the mitochondrial inner membrane, further evidencing its role in mitochondrial transport processes.
SLC19A2 serves as both a thiamine and folic acid transporter at the plasma membrane, contributing to the transport of these vitamins into cells, supporting both thiamine and folic acid metabolic processes.
THTPA functions in the conversion of thiamine triphosphate to thiamine diphosphate, acting as a thiamine triphosphate phosphatase. Involved in broad thiamine metabolic processes, it possesses hydrolase activity, with a focus on dephosphorylation reactions. It has been primarily located in the cytosol.
Anomalous annotations include SLC19A2 being associated with spermatogenesis, which may not directly relate to its primary functions in vitamin transport. Additionally, some annotations suggest contradictory activities, such as SLC25A19 annotations to deoxynucleotide transport, which have been negated in other studies.
Overall, these genes coordinate to manage the cellular and systemic availability of thiamine diphosphate, ensuring proper metabolic processes that utilize this crucial co-factor.
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