PREFIX up: <http://purl.uniprot.org/core/>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
SELECT DISTINCT ?entry ?recName ?geneName WHERE {
  ?entry up:reviewed true .
  ?entry up:recommendedName ?recNameIRI .
  ?recNameIRI up:fullName ?recName .
  ?entry up:encodedBy ?geneIRI .
  ?geneIRI skos:prefLabel ?geneName .
  FILTER ( CONTAINS( LCASE( ?geneName ) , "dna" ) )
}
LIMIT 100

Got 100 rows and 3 columns, showing the first 5 and last 5 rows below:
| entry              | recName                                        | geneName |
| ------------------ | ---------------------------------------------- | -------- |
| uniprot:A0A096MJZ0 | Dynein axonemal light chain 1                  | Dnal1    |
| uniprot:A0A0G2KIZ8 | Dynein axonemal intermediate chain 3           | dnai3    |
| uniprot:A0A1B4XBG5 | Cycloaraneosene synthase sdnA                  | sdnA     |
| uniprot:A0A1L8EYB2 | Dynein axonemal assembly factor 8              | dnaaf8   |
| uniprot:A0A1L8G016 | Dynein axonemal assembly factor 11             | dnaaf11  |
| ...                | ...                                            | ...      |
| uniprot:A1VMG2     | Chaperone protein DnaK                         | dnaK     |
| uniprot:A1VX79     | Chromosomal replication initiator protein DnaA | dnaA     |
| uniprot:A1W0P5     | Chaperone protein DnaJ                         | dnaJ     |
| uniprot:A1WAR6     | Chaperone protein DnaK                         | dnaK     |
| uniprot:A1WAR7     | Chaperone protein DnaJ                         | dnaJ     |

This query returns reviewed UniProtKB entries (Swiss-Prot) and their recommended protein names where the preferred gene name contains the text 'DNA'. The columns are: UniProt entry IRI, recommended protein name, and preferred gene name.

[System]
You are a question answering assistant. Your job is to generate a SPARQL query to answer a given user question.

You have access to the following knowledge graphs:
uniprot at https://qlever.cs.uni-freiburg.de/api/uniprot

You can use the following SPARQL prefixes implicitly in all functions:
ECO: <http://purl.obolibrary.org/obo/ECO_
annotation: <http://purl.uniprot.org/annotation/
bibo: <http://purl.org/ontology/bibo/
busco: <http://busco.ezlab.org/schema#
chebi: <http://purl.obolibrary.org/obo/CHEBI_
citation: <http://purl.uniprot.org/citations/
cito: <http://purl.org/spar/cito/
dcat: <http://www.w3.org/ns/dcat#
dcmit: <http://purl.org/dc/dcmitype/
dcterms: <http://purl.org/dc/terms/
disease: <http://purl.uniprot.org/diseases/
embl-cds: <http://purl.uniprot.org/embl-cds/
ensembl: <http://rdf.ebi.ac.uk/resource/ensembl/
enzyme: <http://purl.uniprot.org/enzyme/
faldo: <http://biohackathon.org/resource/faldo#
foaf: <http://xmlns.com/foaf/0.1/
go: <http://purl.obolibrary.org/obo/GO_
hs: <https://hamap.expasy.org/rdf/vocab#
isoform: <http://purl.uniprot.org/isoforms/
keywords: <http://purl.uniprot.org/keywords/
location: <http://purl.uniprot.org/locations/
obo: <http://purl.obolibrary.org/obo/
oboInOwl: <http://www.geneontology.org/formats/oboInOwl#
owl: <http://www.w3.org/2002/07/owl#
patent: <http://purl.uniprot.org/EPO/
pav: <http://purl.org/pav/
position: <http://purl.uniprot.org/position/
prism: <http://prismstandard.org/namespaces/basic/2.0/
pubmed: <http://purl.uniprot.org/pubmed/
range: <http://purl.uniprot.org/range/
rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#
rdfs: <http://www.w3.org/2000/01/rdf-schema#
rh: <http://rdf.rhea-db.org/
schema: <http://schema.org/
sd: <http://www.w3.org/ns/sparql-service-description#
sh: <http://www.w3.org/ns/shacl#
skos: <http://www.w3.org/2004/02/skos/core#
sp: <http://spinrdf.org/sp#
ssmRegion: <http://purl.uniprot.org/signatureSequenceMatch/
stato: <http://purl.obolibrary.org/obo/STATO_
taxon: <http://purl.uniprot.org/taxonomy/
tissue: <http://purl.uniprot.org/tissues/
uniparc: <http://purl.uniprot.org/uniparc/
uniprot: <http://purl.uniprot.org/uniprot/
up: <http://purl.uniprot.org/core/
voag: <http://voag.linkedmodel.org/schema/voag#
void: <http://rdfs.org/ns/void#
xsd: <http://www.w3.org/2001/XMLSchema#
dc: <http://purl.org/dc/elements/1.1/
prov: <http://www.w3.org/ns/prov#
geo: <http://www.opengis.net/ont/geosparql#
geosparql: <http://www.opengis.net/ont/geosparql#
gn: <http://www.geonames.org/ontology#
bd: <http://www.bigdata.com/rdf#
hint: <http://www.bigdata.com/queryHints#
wikibase: <http://wikiba.se/ontology#
qb: <http://purl.org/linked-data/cube#

You should follow a step-by-step approach to generate the SPARQL query:
1. Determine possible entities and properties implied by the user question.
2. Use the functions to search for entities and properties in the knowledge graphs. Where applicable, constrain the searches with already identified entities and properties.
3. Gradually build up the SPARQL query using the identified entities and properties. Start with simple queries and add more complexity as needed. Use the execute function to get feedback on intermediate queries. You can go back and forth between knowledge graph searches and SPARQL query executions to refine the query.
4. Use the answer or cancel function to finalize your answer and stop the generation process.

Additional rules:
1. Explain your thought process before and after each step and function call.
2. Do not assume or make up any entities or properties without verifying them with the knowledge graphs and functions.
3. The SPARQL query should always return the actual identifiers / IRIs of the items in its result. It additionally may return labels or other human-readable information, but they are optional and should be put within optional clauses unless explicitly requested by the user.
4. Do not stop early if there are still obvious improvements to be made to the SPARQL query. For example, keep refining your SPARQL query if its result contains irrelevant items or is missing items you expected.
5. Do not perform additional computation (e.g. filtering, sorting, calculations) on the result of the SPARQL query to determine the answer. All computation should be done solely within SPARQL.
6. For questions with a "True" or "False" answer the SPARQL query should be an ASK query.
7. Do not use 'SERVICE wikibase:label { bd:serviceParam wikibase:language ...' in SPARQL queries. It is not SPARQL standard and unsupported by the used QLever SPARQL endpoints. Use rdfs:label or similar properties to get labels instead.

[User] Select reviewed UniProtKB entries (Swiss-Prot) and their recommended protein names where the preferred gene name contains the text 'DNA'.

[Assistant]
Let's break down the question:

1. We need UniProtKB entries that are reviewed (Swiss-Prot).
2. For each entry, we want the recommended protein name.
3. The preferred gene name must contain the text 'DNA'.

Step-by-step plan:
- Find how to identify reviewed (Swiss-Prot) entries in UniProt.
- Find how to get the preferred gene name and filter those containing 'DNA'.
- Find how to get the recommended protein name.
- Build a SPARQL query to select the UniProtKB entry and its recommended protein name, filtering as required.

First, let's search for how reviewed (Swiss-Prot) entries are indicated in UniProt.

[Tool]
Top 10 property alternatives:
1. reviewed (up:reviewed): Indicates whether a resource has been reviewed by a curator.
2. created (up:created): The date a resource was created.
3. place of publication (up:place): The place where a publication was published. This usually includes a country name.
4. editor (up:editor): The editor of a publication., has domain Book Citation
5. citation (up:citation): A publication from which data was extracted, or which contains additional information., has range Citation
6. comment (rdfs:comment)
7. complete (up:complete): has domain Taxon
8. complete (busco:complete)
9. abstract (dcterms:abstract)
10. submitted to (up:submittedTo): The database a resource  was submitted to., has domain Submission Citation

[Tool]
No entity items found

No other items found

Top 10 literal alternatives:
1. true: xsd:boolean

[Tool]
Top 10 property alternatives:
1. scientific name (up:scientificName): has domain Taxon
2. name (up:name)
3. allergen name (up:allergenName): See http://www.expasy.org/cgi-bin/lists?allergen.txt
4. common name (up:commonName): has domain Taxon
5. locus name (up:locusName): has domain Gene
6. other name (up:otherName): has domain Taxon
7. CD molecule antigen name (up:cdAntigenName): A name from the Human Cell Differentiation Molecules (HCDM) nomenclature.
8. short name (up:shortName): An abbreviation of the full name or an acronym.
9. namesapce (sh:namesapce)
10. recommended name (up:recommendedName): The name recommended by the UniProt consortium., has range Structured_Name

[Tool]
Top 10 property alternatives:
1. recommended name (up:recommendedName): The name recommended by the UniProt consortium., has range Structured_Name
2. scientific name (up:scientificName): has domain Taxon
3. allergen name (up:allergenName): See http://www.expasy.org/cgi-bin/lists?allergen.txt
4. name (up:name)
5. proteome (up:proteome)
6. proteome component (up:component): A component of a protein., has range Protein part, has domain Protein
7. CD molecule antigen name (up:cdAntigenName): A name from the Human Cell Differentiation Molecules (HCDM) nomenclature.
8. other name (up:otherName): has domain Taxon
9. common name (up:commonName): has domain Taxon
10. panproteome (up:panproteome): The current pan proteome sequences are derived from the referenc...e additional sequences are identified using UniRef50 membership., has domain Proteome, has range Proteome

[Tool]
Top 10 property alternatives:
1. type (rdf:type)
2. label (rdfs:label)
3. is defined by (rdfs:isDefinedBy)
4. comment (rdfs:comment)
5. range (rdfs:range)
6. domain (rdfs:domain)
7. sub property of (rdfs:subPropertyOf)

No other items found

[Tool]
Top 10 property alternatives:
1. type (rdf:type)
2. domain (rdfs:domain)
3. label (rdfs:label)
4. is defined by (rdfs:isDefinedBy)
5. range (rdfs:range)
6. sub property of (rdfs:subPropertyOf)
7. comment (rdfs:comment)

No other items found

[Tool]
Top 10 entity alternatives:
1. Gene (up:Gene)
2. 32630, also known as artificial sequence, synthetic construct, synthetic oligonucleotides, synthetic DNA, synthetic constructs (taxon:32630)
3. 137249, also known as Genea Vittadini 1831, Genea (taxon:137249)
4. 695940, also known as Genea Rondani, 1850, Genea (taxon:695940)
5. 1857509, also known as Genecerus (taxon:1857509)
6. 651458, also known as Geneiorhynchus (taxon:651458)
7. 94189, also known as Genetta (taxon:94189)
8. 94190, also known as GENGE, Genetta genetta, Viverra genetta Linnaeus, 1758, Viverra genetta, Small-spotted genet (taxon:94190)
9. 2005392, also known as synthetic gene (taxon:2005392)
10. negative regulation of gene expression, also known as gene silencing (go:0010629): Any process that decreases the frequency, rate or extent of gene...quence is converted into a mature gene product (protein or RNA).

[Tool]
Top 10 property alternatives:
1. label (rdfs:label)
2. type (rdf:type)
3. is defined by (rdfs:isDefinedBy)
4. sub class of (rdfs:subClassOf)

No other items found

[Tool]
Got 6 rows and 3 columns:
| subject        | property                         | object                 |
| -------------- | -------------------------------- | ---------------------- |
| Gene (up:Gene) | type (rdf:type)                  | class (owl:Class)      |
| Gene (up:Gene) | label (rdfs:label)               | Gene                   |
| Gene (up:Gene) | sub class of (rdfs:subClassOf)   | thing (owl:Thing)      |
| Gene (up:Gene) | is defined by (rdfs:isDefinedBy) | up:                    |
| Gene (up:Gene) | sub class of (rdfs:subClassOf)   | concept (skos:Concept) |
| Gene (up:Gene) | sub class of (rdfs:subClassOf)   | _:bn147                |

[Tool]
Top 10 entity alternatives:
1. name (up:name)
2. Gene (up:Gene)
3. 32630, also known as artificial sequence, synthetic construct, synthetic oligonucleotides, synthetic DNA, synthetic constructs (taxon:32630)
4. 389777, also known as Namea (taxon:389777)
5. 492044, also known as Leptoderma lubricum Abe, Marumo & Kawaguchi, 1965, namera-iwashi, Leptoderma lubricum (taxon:492044)
6. 176187, also known as mafugu, namera-fugu, RMNH:1566, RMNH:D1564-1565 and D1567, Takifugu porphyreus (Temminck & Schlegel, 1850) (taxon:176187)
7. 55571, also known as Dioscorea alata, yam, winged yam, white yam, water yam (taxon:55571)
8. 137249, also known as Genea Vittadini 1831, Genea (taxon:137249)
9. 695940, also known as Genea Rondani, 1850, Genea (taxon:695940)
10. 1857509, also known as Genecerus (taxon:1857509)

[Tool]
Top 10 entity alternatives:
1. Protein (up:Protein): Description of a protein.
2. 448157, also known as 'Proteinimicrobium', Proteinimicrobium (taxon:448157)
3. obsolete protein (go:0003675): OBSOLETE. (Was not defined before being made obsolete).
4. Obsolete Protein (up:Obsolete_Protein)
5. peptidyl-cysteine S-nitrosylation, also known as S-nitrosylation, protein S-nitrosylation (go:0018119): The covalent addition of a nitric oxide (NO) group to the sulphu...ne residue in a protein, to form peptidyl-S-nitrosyl-L-cysteine.
6. peptidyl-lysine modification to peptidyl-hypusine, also known as hypusine anabolism, hypusine formation, hypusine anabolism from peptidyl-lysine, hypusine biosynthesis, hypusine biosynthetic process (go:0008612): The modification of peptidyl-lysine to form hypusine, peptidyl-N6-(4-amino-2-hydroxybutyl)-L-lysine.
7. oxidized purine nucleobase lesion DNA N-glycosylase activity, also known as deoxyribonucleate glycosidase activity, oxidized purine base lesion DNA N-glycosylase activity, purine-specific oxidized base lesion DNA N-glycosylase activity, Fpg protein, formamidopyrimidine-DNA glycosylase activity (go:0008534): Catalysis of the removal of oxidized purine bases by cleaving th...n the cleavage of the DNA backbone 3' of the apurinic (AP) site.
8. modification-dependent protein catabolic process, also known as modification-dependent proteolysis, modification-initiated protein catabolic process, modification-initiated protein catabolism, modification-initiated proteolysis, protein-ligand-dependent protein catabolism (go:0019941): The chemical reactions and pathways resulting in the breakdown o...s, initiated by the covalent modification of the target protein.
9. mRNA guanylyltransferase activity, also known as GTP--RNA guanylyltransferase activity, messenger RNA guanylyltransferase activity, mRNA capping enzyme activity, protein lambda2, GTP:mRNA guanylyltransferase activity (go:0004484): Catalysis of the reaction: GTP + (5')pp-Pur-mRNA = diphosphate +...ugh three phosphates to the 5' position of the terminal residue.
10. nutrient reservoir activity, also known as storage protein, storage protein of fat body, yolk protein (go:0045735): Functions in the storage of nutritious substrates.

[Tool]
Top 10 property alternatives:
1. label (rdfs:label)
2. type (rdf:type)
3. exaple (<http://purl.org/vocab/vann/exaple>)
4. comment (rdfs:comment)
5. sub class of (rdfs:subClassOf)
6. is defined by (rdfs:isDefinedBy)
7. see also (rdfs:seeAlso)
8. disjoint with (owl:disjointWith)

No other items found

[Tool]
Top 10 property alternatives:
1. organism (up:organism): The organism in which a protein occurs., has range Taxon
2. has value (owl:hasValue)
3. has related synonym (oboInOwl:hasRelatedSynonym)
4. scientific name (up:scientificName): has domain Taxon
5. has_score (busco:has_score)
6. part of lineage (up:partOfLineage): True for taxa that can appear as part of an organism's non abbre...ntry (as well as at INSDC) only these taxonomic nodes are shown., has domain Taxon
7. enzyme (up:enzyme): The catalytic activity associated with a protein. or part of a protein., has range Enzyme
8. name (up:name)
9. disease (up:disease): has domain Disease Annotation, has range Disease
10. interaction (up:interaction): has range Interaction, has domain Protein

[Tool]
Top 10 property alternatives:
1. organism (up:organism): The organism in which a protein occurs., has range Taxon
2. enzyme (up:enzyme): The catalytic activity associated with a protein. or part of a protein., has range Enzyme
3. proteome (up:proteome)
4. cofactor (up:cofactor): has domain Cofactor
5. name (up:name)
6. strain (up:strain): has range Taxonomy rank Strain, has range Strain, has domain Taxon
7. scientific name (up:scientificName): has domain Taxon
8. disease (up:disease): has domain Disease Annotation, has range Disease
9. domain (rdfs:domain)
10. domain (up:domain): has range Protein part, A domain of a protein., has domain Protein

[Tool]
Got 65,536 rows and 3 columns, showing the first 10 rows below:
| subject           | property       | object                           |
| ----------------- | -------------- | -------------------------------- |
| citation:1        | name (up:name) | Biochem Med                      |
| citation:100      | name (up:name) | Birth Defects Orig Artic Ser     |
| citation:100133   | name (up:name) | Biochemistry                     |
| citation:1001445  | name (up:name) | FEBS Lett.                       |
| citation:1001817  | name (up:name) | Dev Biol                         |
| citation:1001879  | name (up:name) | Genetics                         |
| citation:1002     | name (up:name) | Biochem. J.                      |
| citation:1002129  | name (up:name) | Hoppe-Seyler's Z. Physiol. Chem. |
| citation:10021329 | name (up:name) | Development                      |
| citation:10021357 | name (up:name) | Curr Biol                        |
| ...               | ...            | ...                              |

[Tool]
Top 10 property alternatives:
1. sub property of (rdfs:subPropertyOf)
2. organism (up:organism): The organism in which a protein occurs., has range Taxon
3. on property (owl:onProperty)
4. scientific name (up:scientificName): has domain Taxon
5. domain (rdfs:domain)
6. domain (up:domain): has range Protein part, A domain of a protein., has domain Protein
7. proteome component (up:component): A component of a protein., has range Protein part, has domain Protein
8. cellular component (up:cellularComponent): has range Cellular Component
9. name (up:name)
10. locus name (up:locusName): has domain Gene

[Tool]
Top 10 property alternatives:
1. annotation (up:annotation): Attaches an annotation to a resource., has range Annotation, has domain Protein
2. proteome (up:proteome)
3. panproteome (up:panproteome): The current pan proteome sequences are derived from the referenc...e additional sequences are identified using UniRef50 membership., has domain Proteome, has range Proteome
4. proteome component (up:component): A component of a protein., has range Protein part, has domain Protein
5. mapped annotation (up:mappedAnnotation): Maps annotation to a resource. Used to link annotations/comments...external non UniProt sources via Citations to UniProt resources., has range Annotation
6. abstract (dcterms:abstract)
7. enzyme class (up:enzymeClass): has domain Catalytic Activity, has range Enzyme
8. organism (up:organism): The organism in which a protein occurs., has range Taxon
9. enzyme (up:enzyme): The catalytic activity associated with a protein. or part of a protein., has range Enzyme
10. coden (bibo:coden)

[Tool]
Got 65,536 rows and 3 columns, showing the first 10 rows below:
| subject            | property                   | object                                                           |
| ------------------ | -------------------------- | ---------------------------------------------------------------- |
| uniprot:A0A000     | annotation (up:annotation) | <http://purl.uniprot.org/uniprot/A0A000#SIP9A1D94175498C8F4>     |
| uniprot:A0A001     | annotation (up:annotation) | <http://purl.uniprot.org/uniprot/A0A001#SIP4C13C9E517FB1E22>     |
| uniprot:A0A002     | annotation (up:annotation) | <http://purl.uniprot.org/uniprot/A0A002#SIP2F1DEBA23C70D39B>     |
| uniprot:A0A003     | annotation (up:annotation) | <http://purl.uniprot.org/uniprot/A0A003#SIP02711004F16CBB1E>     |
| uniprot:A0A004     | annotation (up:annotation) | <http://purl.uniprot.org/uniprot/A0A004#SIP1682853632AF3AAA>     |
| uniprot:A0A006     | annotation (up:annotation) | <http://purl.uniprot.org/uniprot/A0A006#SIP1F01F07BE470EBCF>     |
| uniprot:A0A007     | annotation (up:annotation) | <http://purl.uniprot.org/uniprot/A0A007#SIP088D31B5ABFBCEC4>     |
| uniprot:A0A008     | annotation (up:annotation) | <http://purl.uniprot.org/uniprot/A0A008#SIP4D8E5C96605D3E01>     |
| uniprot:A0A009     | annotation (up:annotation) | <http://purl.uniprot.org/uniprot/A0A009#SIP3D7218B6FB132237>     |
| uniprot:A0A009GKJ5 | annotation (up:annotation) | <http://purl.uniprot.org/uniprot/A0A009GKJ5#SIP4F1081D3688EBAB9> |
| ...                | ...                        | ...                                                              |

[Tool]
Got 51 rows and 3 columns, showing the first 10 rows below:
| subject        | property                              | object                                                                                |
| -------------- | ------------------------------------- | ------------------------------------------------------------------------------------- |
| uniprot:A0A000 | type (rdf:type)                       | Protein (up:Protein)                                                                  |
| uniprot:A0A000 | see also (rdfs:seeAlso)               | <http://purl.uniprot.org/alphafolddb/A0A000>                                          |
| uniprot:A0A000 | modified date (up:modified)           | 2025-02-05 (xsd:date)                                                                 |
| uniprot:A0A000 | version (up:version)                  | 1 (xsd:int)                                                                           |
| uniprot:A0A000 | organism (up:organism)                | 67581 (taxon:67581)                                                                   |
| uniprot:A0A000 | created (up:created)                  | 2006-11-14 (xsd:date)                                                                 |
| uniprot:A0A000 | attribution (up:attribution)          | <http://purl.uniprot.org/uniprot/A0A000#attribution-0B765F33AFD22FB47399EF6A7B86335F> |
| uniprot:A0A000 | reported version (up:reportedVersion) | 1 (xsd:int)                                                                           |
| uniprot:A0A000 | encoded by (up:encodedBy)             | <http://purl.uniprot.org/uniprot/A0A000#gene-MD51BEC367814372C9CF968582089B84D8B>     |
| uniprot:A0A000 | label (rdfs:label)                    | 8-amino-7-oxononanoate synthase                                                       |
| ...            | ...                                   | ...                                                                                |

[Tool]
Got 1 row and 3 columns:
| subject        | property                  | object                                                                            |
| -------------- | ------------------------- | --------------------------------------------------------------------------------- |
| uniprot:A0A000 | encoded by (up:encodedBy) | <http://purl.uniprot.org/uniprot/A0A000#gene-MD51BEC367814372C9CF968582089B84D8B> |

[Tool]
Got 2 rows and 3 columns:
| subject                                                                           | property                    | object         |
| --------------------------------------------------------------------------------- | --------------------------- | -------------- |
| <http://purl.uniprot.org/uniprot/A0A000#gene-MD51BEC367814372C9CF968582089B84D8B> | type (rdf:type)             | Gene (up:Gene) |
| <http://purl.uniprot.org/uniprot/A0A000#gene-MD51BEC367814372C9CF968582089B84D8B> | pref label (skos:prefLabel) | moeA5          |

[Tool]
Got 51 rows and 3 columns, showing the first 10 rows below:
| subject        | property                              | object                                                                                |
| -------------- | ------------------------------------- | ------------------------------------------------------------------------------------- |
| uniprot:A0A000 | type (rdf:type)                       | Protein (up:Protein)                                                                  |
| uniprot:A0A000 | see also (rdfs:seeAlso)               | <http://purl.uniprot.org/alphafolddb/A0A000>                                          |
| uniprot:A0A000 | modified date (up:modified)           | 2025-02-05 (xsd:date)                                                                 |
| uniprot:A0A000 | version (up:version)                  | 1 (xsd:int)                                                                           |
| uniprot:A0A000 | organism (up:organism)                | 67581 (taxon:67581)                                                                   |
| uniprot:A0A000 | created (up:created)                  | 2006-11-14 (xsd:date)                                                                 |
| uniprot:A0A000 | attribution (up:attribution)          | <http://purl.uniprot.org/uniprot/A0A000#attribution-0B765F33AFD22FB47399EF6A7B86335F> |
| uniprot:A0A000 | reported version (up:reportedVersion) | 1 (xsd:int)                                                                           |
| uniprot:A0A000 | encoded by (up:encodedBy)             | <http://purl.uniprot.org/uniprot/A0A000#gene-MD51BEC367814372C9CF968582089B84D8B>     |
| uniprot:A0A000 | label (rdfs:label)                    | 8-amino-7-oxononanoate synthase                                                       |
| ...            | ...                                   | ...                                                                                |

[Tool]
Got 1 row and 3 columns:
| subject        | property               | object              |
| -------------- | ---------------------- | ------------------- |
| uniprot:A0A000 | reviewed (up:reviewed) | false (xsd:boolean) |

[Tool]
Got 65,536 rows and 3 columns, showing the first 10 rows below:
| subject               | property               | object             |
| --------------------- | ---------------------- | ------------------ |
| isoform:A0A024B7W1-1  | reviewed (up:reviewed) | true (xsd:boolean) |
| isoform:A0A061ACU2-1  | reviewed (up:reviewed) | true (xsd:boolean) |
| isoform:A0A061ACU2-10 | reviewed (up:reviewed) | true (xsd:boolean) |
| isoform:A0A061ACU2-11 | reviewed (up:reviewed) | true (xsd:boolean) |
| isoform:A0A061ACU2-12 | reviewed (up:reviewed) | true (xsd:boolean) |
| isoform:A0A061ACU2-2  | reviewed (up:reviewed) | true (xsd:boolean) |
| isoform:A0A061ACU2-3  | reviewed (up:reviewed) | true (xsd:boolean) |
| isoform:A0A061ACU2-4  | reviewed (up:reviewed) | true (xsd:boolean) |
| isoform:A0A061ACU2-5  | reviewed (up:reviewed) | true (xsd:boolean) |
| isoform:A0A061ACU2-6  | reviewed (up:reviewed) | true (xsd:boolean) |
| ...                   | ...                    | ...                |

[Tool]
Got 65,536 rows and 3 columns, showing the first 10 rows below:
| subject            | property                              | object                                                           |
| ------------------ | ------------------------------------- | ---------------------------------------------------------------- |
| uniprot:A0A000     | recommended name (up:recommendedName) | <http://purl.uniprot.org/uniprot/A0A000#SIPB70C697583D4DFF7>     |
| uniprot:A0A004     | recommended name (up:recommendedName) | <http://purl.uniprot.org/uniprot/A0A004#SIPDE8DE3E1F5D42160>     |
| uniprot:A0A006     | recommended name (up:recommendedName) | <http://purl.uniprot.org/uniprot/A0A006#SIPDE8DE3E1F5D42160>     |
| uniprot:A0A009GLU2 | recommended name (up:recommendedName) | <http://purl.uniprot.org/uniprot/A0A009GLU2#SIP9E1560B7A776D307> |
| uniprot:A0A009GN48 | recommended name (up:recommendedName) | <http://purl.uniprot.org/uniprot/A0A009GN48#SIPD2BF893D197D6F98> |
| uniprot:A0A009GNF6 | recommended name (up:recommendedName) | <http://purl.uniprot.org/uniprot/A0A009GNF6#SIPEB54D03AAE812EF2> |
| uniprot:A0A009GNL8 | recommended name (up:recommendedName) | <http://purl.uniprot.org/uniprot/A0A009GNL8#SIPE3CF90C13C0D98CC> |
| uniprot:A0A009GNX9 | recommended name (up:recommendedName) | <http://purl.uniprot.org/uniprot/A0A009GNX9#SIP305559E27EFB5182> |
| uniprot:A0A009GP91 | recommended name (up:recommendedName) | <http://purl.uniprot.org/uniprot/A0A009GP91#SIP1A85407F6B570463> |
| uniprot:A0A009GPG0 | recommended name (up:recommendedName) | <http://purl.uniprot.org/uniprot/A0A009GPG0#SIP983AADAD20AB2C96> |
| ...                | ...                                   | ...                                                              |

[Tool]
Got 3 rows and 3 columns:
| subject                                                      | property                 | object                               |
| ------------------------------------------------------------ | ------------------------ | ------------------------------------ |
| <http://purl.uniprot.org/uniprot/A0A000#SIPB70C697583D4DFF7> | type (rdf:type)          | Structured_Name (up:Structured_Name) |
| <http://purl.uniprot.org/uniprot/A0A000#SIPB70C697583D4DFF7> | fullName (up:fullName)   | 8-amino-7-oxononanoate synthase      |
| <http://purl.uniprot.org/uniprot/A0A000#SIPB70C697583D4DFF7> | EC as a name (up:ecName) | 2.3.1.47                             |

[Tool]
Got 65,536 rows and 3 columns, showing the first 10 rows below:
| subject      | property                    | object                                               |
| ------------ | --------------------------- | ---------------------------------------------------- |
| disease:1    | pref label (skos:prefLabel) | HSD10 mitochondrial disease                          |
| disease:10   | pref label (skos:prefLabel) | Phosphoserine phosphatase deficiency                 |
| disease:100  | pref label (skos:prefLabel) | Amyloidosis, hereditary systemic 1                   |
| disease:1000 | pref label (skos:prefLabel) | Rhegmatogenous retinal detachment autosomal dominant |
| disease:1001 | pref label (skos:prefLabel) | Rhizomelic chondrodysplasia punctata 1               |
| disease:1002 | pref label (skos:prefLabel) | Rhizomelic chondrodysplasia punctata 2               |
| disease:1003 | pref label (skos:prefLabel) | Rhizomelic chondrodysplasia punctata 3               |
| disease:1004 | pref label (skos:prefLabel) | Robinow-Sorauf syndrome                              |
| disease:1005 | pref label (skos:prefLabel) | Rod-cone dystrophy Newfoundland                      |
| disease:1006 | pref label (skos:prefLabel) | Saethre-Chotzen syndrome                             |
| ...          | ...                         | ...                                                  |

[Tool]
Got 100 rows and 3 columns, showing the first 5 and last 5 rows below:
| entry              | recName                                        | geneName |
| ------------------ | ---------------------------------------------- | -------- |
| uniprot:A0A096MJZ0 | Dynein axonemal light chain 1                  | Dnal1    |
| uniprot:A0A0G2KIZ8 | Dynein axonemal intermediate chain 3           | dnai3    |
| uniprot:A0A1B4XBG5 | Cycloaraneosene synthase sdnA                  | sdnA     |
| uniprot:A0A1L8EYB2 | Dynein axonemal assembly factor 8              | dnaaf8   |
| uniprot:A0A1L8G016 | Dynein axonemal assembly factor 11             | dnaaf11  |
| ...                | ...                                            | ...      |
| uniprot:A1VMG2     | Chaperone protein DnaK                         | dnaK     |
| uniprot:A1VX79     | Chromosomal replication initiator protein DnaA | dnaA     |
| uniprot:A1W0P5     | Chaperone protein DnaJ                         | dnaJ     |
| uniprot:A1WAR6     | Chaperone protein DnaK                         | dnaK     |
| uniprot:A1WAR7     | Chaperone protein DnaJ                         | dnaJ     |

[Tool] Stopped generation process

[User]
Feedback (status=done):
The SPARQL query correctly retrieves reviewed UniProtKB entries (Swiss-Prot) and their recommended protein names where the preferred gene name contains the text 'DNA'. The query returns the IRIs of the entries as required, and the additional columns (recommended protein name and gene name) are relevant and not required to be optional since the question asks for them. The use of FILTER(CONTAINS(LCASE(?geneName), "dna")) ensures case-insensitive matching. The output matches the user's request and adheres to the rules.


PREFIX up: <http://purl.uniprot.org/core/>
PREFIX taxon: <http://purl.uniprot.org/taxonomy/>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
SELECT DISTINCT ?protein ?gene ?altGeneName ?altGeneNameType WHERE {
  {
    SELECT DISTINCT ?protein ?gene WHERE {
      ?protein a up:Protein ; up:organism taxon:9606 ; up:encodedBy ?gene .
    }
    LIMIT 5
  }
  {
    ?gene up:orfName ?altGeneName .
    BIND( "orfName" AS ?altGeneNameType )
  } UNION {
    ?gene up:locusName ?altGeneName .
    BIND( "locusName" AS ?altGeneNameType )
  }
  FILTER NOT EXISTS {
    ?gene skos:prefLabel ?altGeneName
  }
}
LIMIT 10

SPARQL execution failed:
Tried to allocate 48.5 GB, but only 12 GB were available. Clear the cache or allow more memory for QLever during startup

Despite multiple attempts to optimize the query by limiting the number of proteins and using subqueries, the UniProt endpoint still runs out of memory when trying to filter alternative gene names that are not recommended (i.e., not equal to the preferred gene name). The data model does not provide a direct 'not recommended' boolean property, so the only way to filter is by comparing alternative names to the preferred name, which is too resource-intensive for the endpoint. A satisfactory SPARQL query cannot be constructed under these constraints.

[System]
You are a question answering assistant. Your job is to generate a SPARQL query to answer a given user question.

You have access to the following knowledge graphs:
uniprot at https://qlever.cs.uni-freiburg.de/api/uniprot

You can use the following SPARQL prefixes implicitly in all functions:
ECO: <http://purl.obolibrary.org/obo/ECO_
annotation: <http://purl.uniprot.org/annotation/
bibo: <http://purl.org/ontology/bibo/
busco: <http://busco.ezlab.org/schema#
chebi: <http://purl.obolibrary.org/obo/CHEBI_
citation: <http://purl.uniprot.org/citations/
cito: <http://purl.org/spar/cito/
dcat: <http://www.w3.org/ns/dcat#
dcmit: <http://purl.org/dc/dcmitype/
dcterms: <http://purl.org/dc/terms/
disease: <http://purl.uniprot.org/diseases/
embl-cds: <http://purl.uniprot.org/embl-cds/
ensembl: <http://rdf.ebi.ac.uk/resource/ensembl/
enzyme: <http://purl.uniprot.org/enzyme/
faldo: <http://biohackathon.org/resource/faldo#
foaf: <http://xmlns.com/foaf/0.1/
go: <http://purl.obolibrary.org/obo/GO_
hs: <https://hamap.expasy.org/rdf/vocab#
isoform: <http://purl.uniprot.org/isoforms/
keywords: <http://purl.uniprot.org/keywords/
location: <http://purl.uniprot.org/locations/
obo: <http://purl.obolibrary.org/obo/
oboInOwl: <http://www.geneontology.org/formats/oboInOwl#
owl: <http://www.w3.org/2002/07/owl#
patent: <http://purl.uniprot.org/EPO/
pav: <http://purl.org/pav/
position: <http://purl.uniprot.org/position/
prism: <http://prismstandard.org/namespaces/basic/2.0/
pubmed: <http://purl.uniprot.org/pubmed/
range: <http://purl.uniprot.org/range/
rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#
rdfs: <http://www.w3.org/2000/01/rdf-schema#
rh: <http://rdf.rhea-db.org/
schema: <http://schema.org/
sd: <http://www.w3.org/ns/sparql-service-description#
sh: <http://www.w3.org/ns/shacl#
skos: <http://www.w3.org/2004/02/skos/core#
sp: <http://spinrdf.org/sp#
ssmRegion: <http://purl.uniprot.org/signatureSequenceMatch/
stato: <http://purl.obolibrary.org/obo/STATO_
taxon: <http://purl.uniprot.org/taxonomy/
tissue: <http://purl.uniprot.org/tissues/
uniparc: <http://purl.uniprot.org/uniparc/
uniprot: <http://purl.uniprot.org/uniprot/
up: <http://purl.uniprot.org/core/
voag: <http://voag.linkedmodel.org/schema/voag#
void: <http://rdfs.org/ns/void#
xsd: <http://www.w3.org/2001/XMLSchema#
dc: <http://purl.org/dc/elements/1.1/
prov: <http://www.w3.org/ns/prov#
geo: <http://www.opengis.net/ont/geosparql#
geosparql: <http://www.opengis.net/ont/geosparql#
gn: <http://www.geonames.org/ontology#
bd: <http://www.bigdata.com/rdf#
hint: <http://www.bigdata.com/queryHints#
wikibase: <http://wikiba.se/ontology#
qb: <http://purl.org/linked-data/cube#

You should follow a step-by-step approach to generate the SPARQL query:
1. Determine possible entities and properties implied by the user question.
2. Use the functions to search for entities and properties in the knowledge graphs. Where applicable, constrain the searches with already identified entities and properties.
3. Gradually build up the SPARQL query using the identified entities and properties. Start with simple queries and add more complexity as needed. Use the execute function to get feedback on intermediate queries. You can go back and forth between knowledge graph searches and SPARQL query executions to refine the query.
4. Use the answer or cancel function to finalize your answer and stop the generation process.

Additional rules:
1. Explain your thought process before and after each step and function call.
2. Do not assume or make up any entities or properties without verifying them with the knowledge graphs and functions.
3. The SPARQL query should always return the actual identifiers / IRIs of the items in its result. It additionally may return labels or other human-readable information, but they are optional and should be put within optional clauses unless explicitly requested by the user.
4. Do not stop early if there are still obvious improvements to be made to the SPARQL query. For example, keep refining your SPARQL query if its result contains irrelevant items or is missing items you expected.
5. Do not perform additional computation (e.g. filtering, sorting, calculations) on the result of the SPARQL query to determine the answer. All computation should be done solely within SPARQL.
6. For questions with a "True" or "False" answer the SPARQL query should be an ASK query.
7. Do not use 'SERVICE wikibase:label { bd:serviceParam wikibase:language ...' in SPARQL queries. It is not SPARQL standard and unsupported by the used QLever SPARQL endpoints. Use rdfs:label or similar properties to get labels instead.

[User] List UniProtKB proteins with their associated genes and the alternative gene names that are used but not recommended by UniProtKB.

[Assistant]
Let's break down the question:

1. We need UniProtKB proteins (entities of type up:Protein).
2. For each protein, we want the associated gene(s).
3. For each gene, we want alternative gene names that are "used" but "not recommended" by UniProtKB.

Let's clarify the relevant properties:
- Proteins are linked to genes via up:encodedBy or up:gene.
- Gene names and their types (primary, synonym, etc.) are modeled in UniProt RDF using up:Gene and up:GeneName, with up:geneNameType indicating the type (e.g., "primary", "synonym", "ordered locus", "ORF", etc.).
- "Used but not recommended" gene names are typically those with up:geneNameType "synonym".

To be sure, let's search for gene name type properties and values to confirm the correct usage.

[Tool]
Top 10 property alternatives:
1. scientific name (up:scientificName): has domain Taxon
2. type (rdf:type)
3. CD molecule antigen name (up:cdAntigenName): A name from the Human Cell Differentiation Molecules (HCDM) nomenclature.
4. allergen name (up:allergenName): See http://www.expasy.org/cgi-bin/lists?allergen.txt
5. common name (up:commonName): has domain Taxon
6. name (up:name)
7. organism (up:organism): The organism in which a protein occurs., has range Taxon
8. other name (up:otherName): has domain Taxon
9. locus name (up:locusName): has domain Gene
10. structured name type (up:structuredNameType): All names of the protein, from commonly used to obsolete, to used in the literature.., has domain Structured_Name

[Tool]
Top 10 property alternatives:
1. scientific name (up:scientificName): has domain Taxon
2. name (up:name)
3. allergen name (up:allergenName): See http://www.expasy.org/cgi-bin/lists?allergen.txt
4. common name (up:commonName): has domain Taxon
5. locus name (up:locusName): has domain Gene
6. other name (up:otherName): has domain Taxon
7. CD molecule antigen name (up:cdAntigenName): A name from the Human Cell Differentiation Molecules (HCDM) nomenclature.
8. short name (up:shortName): An abbreviation of the full name or an acronym.
9. namesapce (sh:namesapce)
10. recommended name (up:recommendedName): The name recommended by the UniProt consortium., has range Structured_Name

[Tool]
Top 10 property alternatives:
1. organism (up:organism): The organism in which a protein occurs., has range Taxon
2. enzyme (up:enzyme): The catalytic activity associated with a protein. or part of a protein., has range Enzyme
3. proteome (up:proteome)
4. cofactor (up:cofactor): has domain Cofactor
5. name (up:name)
6. strain (up:strain): has range Taxonomy rank Strain, has range Strain, has domain Taxon
7. scientific name (up:scientificName): has domain Taxon
8. disease (up:disease): has domain Disease Annotation, has range Disease
9. domain (rdfs:domain)
10. domain (up:domain): has range Protein part, A domain of a protein., has domain Protein

[Tool]
Top 10 property alternatives:
1. label (rdfs:label)
2. type (rdf:type)
3. is defined by (rdfs:isDefinedBy)
4. sub class of (rdfs:subClassOf)

No other items found

[Tool]
Got 6 rows and 3 columns:
| subject        | property                         | object                 |
| -------------- | -------------------------------- | ---------------------- |
| Gene (up:Gene) | type (rdf:type)                  | class (owl:Class)      |
| Gene (up:Gene) | label (rdfs:label)               | Gene                   |
| Gene (up:Gene) | sub class of (rdfs:subClassOf)   | thing (owl:Thing)      |
| Gene (up:Gene) | is defined by (rdfs:isDefinedBy) | up:                    |
| Gene (up:Gene) | sub class of (rdfs:subClassOf)   | concept (skos:Concept) |
| Gene (up:Gene) | sub class of (rdfs:subClassOf)   | _:bn147                |

[Tool]
Top 10 property alternatives:
1. encoded by (up:encodedBy): The gene by which a protein is encoded., has domain Protein, has range Gene
2. encoded in (up:encodedIn): The subcellular location where a protein is encoded., has range Subcellular Location, has domain Protein
3. coden (bibo:coden)
4. identifier (dcterms:identifier)
5. shortCoden (up:shortCoden): Used to link a Journal to its shortCoden, has domain Journal
6. Mnemonic (up:mnemonic): A easy to remember identifier for a UniProtKB entry, but it is n...entifier and should not be used by programs to identify entries., A rememberable string that can be used to find entries, not a stable identifier!
7. link is explicit (up:linkIsExplicit): True if the Database is linked by an explicit action to UniProt, false if it is done using a simple hardcoded rule., has domain Database (description of)
8. label (rdfs:label)
9. type (rdf:type)
10. exact match (skos:exactMatch)

[Tool]
Top 10 property alternatives:
1. synonym (up:synonym): has domain Taxon
2. organism (up:organism): The organism in which a protein occurs., has range Taxon
3. other name (up:otherName): has domain Taxon
4. has exact synonym (oboInOwl:hasExactSynonym)
5. common name (up:commonName): has domain Taxon
6. abbreviation (up:abbreviation)
7. scientific name (up:scientificName): has domain Taxon
8. has related synonym (oboInOwl:hasRelatedSynonym)
9. recommended name (up:recommendedName): The name recommended by the UniProt consortium., has range Structured_Name
10. alternativeName (up:alternativeName): A synonym of the recommended name., has range Structured_Name

[Tool]
Top 10 property alternatives:
1. alternativeName (up:alternativeName): A synonym of the recommended name., has range Structured_Name
2. other name (up:otherName): has domain Taxon
3. scientific name (up:scientificName): has domain Taxon
4. recommended name (up:recommendedName): The name recommended by the UniProt consortium., has range Structured_Name
5. abbreviation (up:abbreviation)
6. common name (up:commonName): has domain Taxon
7. allergen name (up:allergenName): See http://www.expasy.org/cgi-bin/lists?allergen.txt
8. CD molecule antigen name (up:cdAntigenName): A name from the Human Cell Differentiation Molecules (HCDM) nomenclature.
9. name (up:name)
10. short name (up:shortName): An abbreviation of the full name or an acronym.

[Tool]
Top 10 property alternatives:
1. type (rdf:type)
2. sub class of (rdfs:subClassOf)
3. label (rdfs:label)
4. is defined by (rdfs:isDefinedBy)

No other items found

[Tool]
Top 10 property alternatives:
1. organism (up:organism): The organism in which a protein occurs., has range Taxon
2. enzyme (up:enzyme): The catalytic activity associated with a protein. or part of a protein., has range Enzyme
3. proteome (up:proteome)
4. cofactor (up:cofactor): has domain Cofactor
5. name (up:name)
6. strain (up:strain): has range Taxonomy rank Strain, has range Strain, has domain Taxon
7. scientific name (up:scientificName): has domain Taxon
8. disease (up:disease): has domain Disease Annotation, has range Disease
9. domain (rdfs:domain)
10. domain (up:domain): has range Protein part, A domain of a protein., has domain Protein

[Tool]
Got 65,536 rows and 3 columns, showing the first 10 rows below:
| subject                                     | property                  | object                                                                            |
| ------------------------------------------- | ------------------------- | --------------------------------------------------------------------------------- |
| <http://purl.uniprot.org/EMBL_CON/AAB06448> | encoded by (up:encodedBy) | <http://purl.uniprot.org/EMBL_CON/AAB06448#gene-CD22>                             |
| <http://purl.uniprot.org/EMBL_CON/AAB06449> | encoded by (up:encodedBy) | <http://purl.uniprot.org/EMBL_CON/AAB06449#gene-CD22>                             |
| <http://purl.uniprot.org/EMBL_CON/AAB18828> | encoded by (up:encodedBy) | <http://purl.uniprot.org/EMBL_CON/AAB18828#gene-FMR1>                             |
| <http://purl.uniprot.org/EMBL_CON/AAB18829> | encoded by (up:encodedBy) | <http://purl.uniprot.org/EMBL_CON/AAB18829#gene-FMR1>                             |
| <http://purl.uniprot.org/EMBL_CON/AAB18830> | encoded by (up:encodedBy) | <http://purl.uniprot.org/EMBL_CON/AAB18830#gene-FMR1>                             |
| <http://purl.uniprot.org/EMBL_CON/AAB18831> | encoded by (up:encodedBy) | <http://purl.uniprot.org/EMBL_CON/AAB18831#gene-FMR1>                             |
| <http://purl.uniprot.org/EMBL_CON/AAB18832> | encoded by (up:encodedBy) | <http://purl.uniprot.org/EMBL_CON/AAB18832#gene-FMR1>                             |
| <http://purl.uniprot.org/EMBL_CON/AAB18833> | encoded by (up:encodedBy) | <http://purl.uniprot.org/EMBL_CON/AAB18833#gene-FMR1>                             |
| <http://purl.uniprot.org/EMBL_CON/AAB46340> | encoded by (up:encodedBy) | <http://purl.uniprot.org/EMBL_CON/AAB46340#gene-CFTR>                             |
| <http://purl.uniprot.org/EMBL_CON/AAB46344> | encoded by (up:encodedBy) | <http://purl.uniprot.org/EMBL_CON/AAB46344#gene-C31FCF0A7CB2E3DEEC0ECD4037C23A97> |
| ...                                         | ...                       | ...                                                                               |

[Tool]
Got 2 rows and 3 columns:
| subject                                               | property                    | object         |
| ----------------------------------------------------- | --------------------------- | -------------- |
| <http://purl.uniprot.org/EMBL_CON/AAB06448#gene-CD22> | type (rdf:type)             | Gene (up:Gene) |
| <http://purl.uniprot.org/EMBL_CON/AAB06448#gene-CD22> | pref label (skos:prefLabel) | CD22           |

[Tool]
Got 2 rows and 3 columns:
| subject                                               | property                    | object         |
| ----------------------------------------------------- | --------------------------- | -------------- |
| <http://purl.uniprot.org/EMBL_CON/AAB06448#gene-CD22> | type (rdf:type)             | Gene (up:Gene) |
| <http://purl.uniprot.org/EMBL_CON/AAB06448#gene-CD22> | pref label (skos:prefLabel) | CD22           |

[Tool]
Got 65,536 rows and 3 columns, showing the first 10 rows below:
| subject            | property                             | object                                                           |
| ------------------ | ------------------------------------ | ---------------------------------------------------------------- |
| uniprot:A0A009GN48 | alternativeName (up:alternativeName) | <http://purl.uniprot.org/uniprot/A0A009GN48#SIPA03F5F491FF17AEA> |
| uniprot:A0A009GQ90 | alternativeName (up:alternativeName) | <http://purl.uniprot.org/uniprot/A0A009GQ90#SIP451B5D3EBBD91A7E> |
| uniprot:A0A009GQN0 | alternativeName (up:alternativeName) | <http://purl.uniprot.org/uniprot/A0A009GQN0#SIP42AA6A17FF2F6FE5> |
| uniprot:A0A009GR33 | alternativeName (up:alternativeName) | <http://purl.uniprot.org/uniprot/A0A009GR33#SIP4969AB370690F1B9> |
| uniprot:A0A009GT53 | alternativeName (up:alternativeName) | <http://purl.uniprot.org/uniprot/A0A009GT53#SIP8565CFD81061D792> |
| uniprot:A0A009GT59 | alternativeName (up:alternativeName) | <http://purl.uniprot.org/uniprot/A0A009GT59#SIP0D785C802095B2DC> |
| uniprot:A0A009GTR2 | alternativeName (up:alternativeName) | <http://purl.uniprot.org/uniprot/A0A009GTR2#SIP03E67624775BD995> |
| uniprot:A0A009GU80 | alternativeName (up:alternativeName) | <http://purl.uniprot.org/uniprot/A0A009GU80#SIPE73F03AA809372EC> |
| uniprot:A0A009GU89 | alternativeName (up:alternativeName) | <http://purl.uniprot.org/uniprot/A0A009GU89#SIP0249CFB8AFA1BDBE> |
| uniprot:A0A009GU91 | alternativeName (up:alternativeName) | <http://purl.uniprot.org/uniprot/A0A009GU91#SIP07B853ED29FE9CE8> |
| ...                | ...                                  | ...                                                              |

[Tool]
Got 74 rows and 3 columns, showing the first 10 rows below:
| subject            | property                              | object                                                                                |
| ------------------ | ------------------------------------- | ----------------------------------------------------------------------------------------- |
| uniprot:A0A009GN48 | type (rdf:type)                       | Protein (up:Protein)                                                                      |
| uniprot:A0A009GN48 | see also (rdfs:seeAlso)               | <http://purl.uniprot.org/alphafolddb/A0A009GN48>                                          |
| uniprot:A0A009GN48 | modified date (up:modified)           | 2025-02-05 (xsd:date)                                                                     |
| uniprot:A0A009GN48 | version (up:version)                  | 1 (xsd:int)                                                                               |
| uniprot:A0A009GN48 | organism (up:organism)                | 1310608 (taxon:1310608)                                                                   |
| uniprot:A0A009GN48 | created (up:created)                  | 2014-06-11 (xsd:date)                                                                     |
| uniprot:A0A009GN48 | attribution (up:attribution)          | <http://purl.uniprot.org/uniprot/A0A009GN48#attribution-0233A437C78A86A79EF6636B5B724269> |
| uniprot:A0A009GN48 | reported version (up:reportedVersion) | 1 (xsd:int)                                                                               |
| uniprot:A0A009GN48 | encoded by (up:encodedBy)             | <http://purl.uniprot.org/uniprot/A0A009GN48#gene-MD5696097372AB4546406FB7F8914C8C53D>     |
| uniprot:A0A009GN48 | proteome (up:proteome)                | <http://purl.uniprot.org/proteomes/UP000022741#Unassembled%20WGS%20sequence>              |
| ...                | ...                                   | ...                                                                                |

[Tool]
Got 2 rows and 3 columns:
| subject                                                                               | property              | object         |
| ------------------------------------------------------------------------------------- | --------------------- | -------------- |
| <http://purl.uniprot.org/uniprot/A0A009GN48#gene-MD5696097372AB4546406FB7F8914C8C53D> | type (rdf:type)       | Gene (up:Gene) |
| <http://purl.uniprot.org/uniprot/A0A009GN48#gene-MD5696097372AB4546406FB7F8914C8C53D> | ORF name (up:orfName) | J507_3974      |

[Tool]
Got 2 rows and 3 columns:
| subject                                                                               | property              | object         |
| ------------------------------------------------------------------------------------- | --------------------- | -------------- |
| <http://purl.uniprot.org/uniprot/A0A009GN48#gene-MD5696097372AB4546406FB7F8914C8C53D> | type (rdf:type)       | Gene (up:Gene) |
| <http://purl.uniprot.org/uniprot/A0A009GN48#gene-MD5696097372AB4546406FB7F8914C8C53D> | ORF name (up:orfName) | J507_3974      |

[Tool]
Got 65,536 rows and 3 columns, showing the first 10 rows below:
| subject                                                                               | property              | object    |
| ------------------------------------------------------------------------------------- | --------------------- | --------- |
| <http://purl.uniprot.org/uniprot/A0A009GKJ5#gene-MD56A0F21E780724EEA22168E5549F77EE6> | ORF name (up:orfName) | J507_4090 |
| <http://purl.uniprot.org/uniprot/A0A009GKR3#gene-MD51C4883E2D9FC4118EAE99B33B7F006FC> | ORF name (up:orfName) | J507_4088 |
| <http://purl.uniprot.org/uniprot/A0A009GL10#gene-MD539D924E685EB41E264E126E519BCD159> | ORF name (up:orfName) | J507_4083 |
| <http://purl.uniprot.org/uniprot/A0A009GL41#gene-MD5744593451E57535DE6809E04EF6DE493> | ORF name (up:orfName) | J507_2815 |
| <http://purl.uniprot.org/uniprot/A0A009GL87#gene-MD50D8409C6E057EDD0B3A02D0526E8B688> | ORF name (up:orfName) | J507_4075 |
| <http://purl.uniprot.org/uniprot/A0A009GLJ5#gene-MD57D7935FF72B1CA80A1793482971D5AEF> | ORF name (up:orfName) | J507_2437 |
| <http://purl.uniprot.org/uniprot/A0A009GLU2#gene-MD5A9A9E7379DE69FC8C9E7BEE91CE97E61> | ORF name (up:orfName) | J507_4041 |
| <http://purl.uniprot.org/uniprot/A0A009GMH1#gene-MD5D5B83D33B22BEADF9271A803C1418A87> | ORF name (up:orfName) | J507_4016 |
| <http://purl.uniprot.org/uniprot/A0A009GMR1#gene-MD59452547B45058C01098EEC79B6AB7345> | ORF name (up:orfName) | J507_3998 |
| <http://purl.uniprot.org/uniprot/A0A009GMU8#gene-MD5299D74E5C88F180F25EBA7F28E025AF2> | ORF name (up:orfName) | J507_3992 |
| ...                                                                                | ...                   | ...       |

[Tool]
Got 65,536 rows and 3 columns, showing the first 10 rows below:
| subject                                                                               | property                  | object      |
| ------------------------------------------------------------------------------------- | ------------------------- | ----------- |
| <http://purl.uniprot.org/uniprot/A0A023GPJ0#gene-MD551A20C064C1113176919BE6A2FB7700F> | locus name (up:locusName) | ECL_04450.1 |
| <http://purl.uniprot.org/uniprot/A0A023PXA5#gene-MD5BF0112EEF2B49D4DB6C562DBA8DD69AD> | locus name (up:locusName) | YAL019W-A   |
| <http://purl.uniprot.org/uniprot/A0A023PXB0#gene-MD50A37FEAEE80361ADEC35E557372837ED> | locus name (up:locusName) | YAR019W-A   |
| <http://purl.uniprot.org/uniprot/A0A023PXB5#gene-MD5B49ECC74A28A625345C416383DEBAB5F> | locus name (up:locusName) | YDR112W     |
| <http://purl.uniprot.org/uniprot/A0A023PXB9#gene-MD54D93339A79521B81E51BAEF2212622B2> | locus name (up:locusName) | YDR199W     |
| <http://purl.uniprot.org/uniprot/A0A023PXC2#gene-MD5835020876BC8375184DC0134D2F40D5C> | locus name (up:locusName) | YEL053W-A   |
| <http://purl.uniprot.org/uniprot/A0A023PXC7#gene-MD5386A78C0FECF5318427FF0883A67AE07> | locus name (up:locusName) | YER068C-A   |
| <http://purl.uniprot.org/uniprot/A0A023PXD3#gene-MD5409F958ED9282577BF18BD45A9EF02E6> | locus name (up:locusName) | YER088C-A   |
| <http://purl.uniprot.org/uniprot/A0A023PXD5#gene-MD5869744E7AE225DE6F562ADE07E12EF8A> | locus name (up:locusName) | YER147C-A   |
| <http://purl.uniprot.org/uniprot/A0A023PXD9#gene-MD531B16F2B23A0BC906A347074AE62F120> | locus name (up:locusName) | YFL015W-A   |
| ...                                                                                | ...                       | ...         |

[Tool] Got no rows and 3 columns

[Tool]
Got 65,536 rows and 3 columns, showing the first 10 rows below:
| subject            | property                              | object                                                           |
| ------------------ | ------------------------------------- | ---------------------------------------------------------------- |
| uniprot:A0A000     | recommended name (up:recommendedName) | <http://purl.uniprot.org/uniprot/A0A000#SIPB70C697583D4DFF7>     |
| uniprot:A0A004     | recommended name (up:recommendedName) | <http://purl.uniprot.org/uniprot/A0A004#SIPDE8DE3E1F5D42160>     |
| uniprot:A0A006     | recommended name (up:recommendedName) | <http://purl.uniprot.org/uniprot/A0A006#SIPDE8DE3E1F5D42160>     |
| uniprot:A0A009GLU2 | recommended name (up:recommendedName) | <http://purl.uniprot.org/uniprot/A0A009GLU2#SIP9E1560B7A776D307> |
| uniprot:A0A009GN48 | recommended name (up:recommendedName) | <http://purl.uniprot.org/uniprot/A0A009GN48#SIPD2BF893D197D6F98> |
| uniprot:A0A009GNF6 | recommended name (up:recommendedName) | <http://purl.uniprot.org/uniprot/A0A009GNF6#SIPEB54D03AAE812EF2> |
| uniprot:A0A009GNL8 | recommended name (up:recommendedName) | <http://purl.uniprot.org/uniprot/A0A009GNL8#SIPE3CF90C13C0D98CC> |
| uniprot:A0A009GNX9 | recommended name (up:recommendedName) | <http://purl.uniprot.org/uniprot/A0A009GNX9#SIP305559E27EFB5182> |
| uniprot:A0A009GP91 | recommended name (up:recommendedName) | <http://purl.uniprot.org/uniprot/A0A009GP91#SIP1A85407F6B570463> |
| uniprot:A0A009GPG0 | recommended name (up:recommendedName) | <http://purl.uniprot.org/uniprot/A0A009GPG0#SIP983AADAD20AB2C96> |
| ...                | ...                                   | ...                                                              |

[Tool] Constraint "uniprot:A0A009GN48#SIPA03F5F491FF17AEA" for subject position is not a valid IRI. IRIs can be given in prefixed form, like "wd:Q937", as URIs, like "http://www.wikidata.org/entity/Q937", or in full form, like "<http://www.wikidata.org/entity/Q937>".

[Tool]
Got 2 rows and 3 columns:
| subject                                                          | property               | object                               |
| ---------------------------------------------------------------- | ---------------------- | ------------------------------------ |
| <http://purl.uniprot.org/uniprot/A0A009GN48#SIPA03F5F491FF17AEA> | type (rdf:type)        | Structured_Name (up:Structured_Name) |
| <http://purl.uniprot.org/uniprot/A0A009GN48#SIPA03F5F491FF17AEA> | fullName (up:fullName) | DNA 3'-5' helicase II                |

[Assistant]
Here's my summary of the data model and how to answer the question:

- UniProtKB proteins are instances of up:Protein (e.g., uniprot:A0A009GN48).
- Each protein is linked to one or more genes via up:encodedBy, whose object is a gene node (e.g., <http://purl.uniprot.org/uniprot/A0A009GN48#gene-MD5696097372AB4546406FB7F8914C8C53D>).
- Genes have properties such as up:orfName and up:locusName, which are alternative gene names.
- The preferred gene name is not explicitly labeled as such, but alternative names are given by up:orfName and up:locusName.
- up:alternativeName on the protein refers to alternative protein names, not gene names.

Therefore, to answer the question, I will:
- List proteins (up:Protein).
- For each, get associated gene(s) via up:encodedBy.
- For each gene, get up:orfName and up:locusName, which are alternative gene names (used but not recommended).
- Optionally, get the preferred gene name if available (skos:prefLabel).

Now, I'll write a SPARQL query that retrieves:
- Protein IRI
- Gene IRI
- Alternative gene names (up:orfName and up:locusName)
- Optionally, the preferred gene name (skos:prefLabel)

Here's the query:

[Tool] Stopped generation process

[User]
Feedback (status=retry):
The SPARQL query failed due to memory limitations on the endpoint, likely because it attempts to retrieve a large number of proteins and associated gene names without sufficient filtering. To improve this, consider adding more restrictive filters (e.g., limiting to a specific organism, protein family, or gene type) or retrieving a smaller subset of proteins. Additionally, ensure the query is as efficient as possible by minimizing OPTIONAL clauses and using FILTERs judiciously. The current query cannot be evaluated for correctness due to the execution failure, so it needs to be retried with optimizations or constraints to reduce resource usage.

[Assistant]
Thank you for the feedback. To address the memory issue, I will:
- Restrict the query to a specific organism (for example, Homo sapiens, taxon:9606).
- Reduce the use of OPTIONAL clauses by focusing only on retrieving alternative gene names (up:orfName and up:locusName).
- Limit the result set further (e.g., LIMIT 50).

First, I need to confirm the correct property for organism and the IRI for Homo sapiens. I'll search for "Homo sapiens" in UniProt.

[Tool]
Top 10 entity alternatives:
1. 9606, also known as Homo sapiens, Humo sapiens, Homo spiens, Homo spaiens, Homo sapines (taxon:9606)
2. 63221, also known as Homo sapiens neanderthalensis, Neanderthal man, Neanderthal 1, Neandertal man, Neandertal (taxon:63221)
3. 741158, also known as Denisova hominin, Homo sapiens subsp. 'Denisova', Homo sp. Altai, Homo sapiens ssp. Denisova, Denisovans (taxon:741158)
4. 2665953, also known as Homo sapiens environmental sample (taxon:2665953)
5. 1383439, also known as Homo sapiens/Mus musculus xenograft (taxon:1383439)
6. 1573476, also known as Homo sapiens/Rattus norvegicus xenograft (taxon:1573476)
7. 1131344, also known as Homo sapiens x Mus musculus, Homo sapiens x Mus musculus hybrid cell line (taxon:1131344)
8. 1035824, also known as Trichuris sp. ex Homo sapiens JP-2011 (taxon:1035824)
9. 2045059, also known as Homo sapiens x Rattus norvegicus fusion cell line (taxon:2045059)
10. 9605, also known as Homo Linnaeus, 1758, humans, Homo (taxon:9605)

[Tool]
Top 10 property alternatives:
1. organism (up:organism): The organism in which a protein occurs., has range Taxon
2. common taxon (up:commonTaxon): has domain Cluster (UniRef), has range Taxon
3. object (rdf:object)
4. type (rdf:type)
5. strain (up:strain): has range Taxonomy rank Strain, has range Strain, has domain Taxon
6. cellular component (up:cellularComponent): has range Cellular Component
7. enzyme (up:enzyme): The catalytic activity associated with a protein. or part of a protein., has range Enzyme
8. scientific name (up:scientificName): has domain Taxon
9. proteome (up:proteome)
10. proteome component (up:component): A component of a protein., has range Protein part, has domain Protein

[Tool]
Got 50 rows and 4 columns, showing the first 5 and last 5 rows below:
| protein            | gene                                                                                | altGeneName | altGeneNameType |
| ------------------ | ------------------------------------------------------------------------------------- | ----------- | --------------- |
| uniprot:A0A023T6R1 | <http://purl.uniprot.org/uniprot/A0A023T6R1#gene-MD54DFAB9C95E12948C8C1EF485BE21A605> | hCG_1773848 | orfName         |
| uniprot:A0A024QY88 | <http://purl.uniprot.org/uniprot/A0A024QY88#gene-MD531404CCE810FB151A15BB72574247F6A> | hCG_14780   | orfName         |
| uniprot:A0A024QYR8 | <http://purl.uniprot.org/uniprot/A0A024QYR8#gene-MD53A00739C97D9351F912DBF6B61B3A86A> | hCG_27750   | orfName         |
| uniprot:A0A024QZ33 | <http://purl.uniprot.org/uniprot/A0A024QZ33#gene-MD5B919DB612F54D222CEFC1DC5A2616314> | hCG_1646942 | orfName         |
| uniprot:A0A024QZ42 | <http://purl.uniprot.org/uniprot/A0A024QZ42#gene-MD5E8FCCBA75147FAACB200D9960C09E296> | hCG_1985580 | orfName         |
| ...                | ...                                                                                | ...         | ...             |
| uniprot:A0A024R571 | <http://purl.uniprot.org/uniprot/A0A024R571#gene-MD5F903707E12C1044274D788B4D4F6455C> | hCG_23386   | orfName         |
| uniprot:A0A024R579 | <http://purl.uniprot.org/uniprot/A0A024R579#gene-MD536DA32439C5DCAD202F62E11D0467B51> | hCG_23404   | orfName         |
| uniprot:A0A024R5F7 | <http://purl.uniprot.org/uniprot/A0A024R5F7#gene-MD51688AF40907EEE2B172EBD17FC89568A> | hCG_2017142 | orfName         |
| uniprot:A0A024R5G9 | <http://purl.uniprot.org/uniprot/A0A024R5G9#gene-MD54449C2D777EA8296EB22F0FD6CD600B2> | hCG_20245   | orfName         |
| uniprot:A0A024R5J5 | <http://purl.uniprot.org/uniprot/A0A024R5J5#gene-MD5DD4B15EA443E6C9DDDF26F541680342A> | hCG_1773959 | orfName         |

[Tool] Stopped generation process

[User]
Feedback (status=refine):
The query correctly retrieves UniProtKB proteins, their associated genes, and alternative gene names (ORF and locus names) for Homo sapiens. However, the user specifically asked for alternative gene names that are 'used but not recommended by UniProtKB.' The current query does not check whether these names are not recommended; it simply retrieves all ORF and locus names. To fully satisfy the user's request, the query should filter for alternative gene names that are explicitly marked as 'not recommended' in the UniProtKB data model (if such a property exists, e.g., up:recommendedName false or similar). Please refine the query to include this filter if possible.

[Assistant]
Thank you for the feedback. The goal is to retrieve only those gene names that are explicitly "not recommended" by UniProtKB, if such a distinction exists in the data model.

From previous exploration:
- up:recommendedName is used for recommended names (but for proteins, not genes).
- For genes, alternative names (up:orfName, up:locusName) are typically not recommended, while the preferred name may be given as skos:prefLabel.
- There does not appear to be an explicit boolean property marking a gene name as "recommended" or "not recommended"—rather, the presence of skos:prefLabel seems to indicate the recommended name, while up:orfName and up:locusName are alternative (not recommended) names.

To ensure we only return alternative gene names that are not recommended, I will:
- Retrieve all up:orfName and up:locusName for each gene.
- Exclude any alternative gene name that matches the preferred gene name (skos:prefLabel), if present.

I will implement this logic in the query by:
- Optionally retrieving the preferred gene name (skos:prefLabel).
- Filtering out any alternative gene name that is equal to the preferred gene name.

Let's proceed with this refined query.

[Tool]
SPARQL execution failed:
Tried to allocate 48.5 GB, but only 8.1 GB were available. Clear the cache or allow more memory for QLever during startup

[Assistant]
The refined query is still too resource-intensive due to the OPTIONAL and FILTER logic across a large dataset. To further optimize, I will:

- Remove the OPTIONAL clause and instead use a subquery to retrieve the preferred gene name for each gene, then join only where the alternative name is not equal to the preferred name.
- Limit the number of proteins processed by adding a subquery with LIMIT.

Here’s the revised plan:
1. Select a limited set of proteins from Homo sapiens.
2. For each, get the associated gene and its preferred name (if any).
3. Retrieve alternative gene names (up:orfName, up:locusName) that do not match the preferred name.

Let’s implement this with a subquery for efficiency.

[Tool]
SPARQL execution failed:
Tried to allocate 48.5 GB, but only 12 GB were available. Clear the cache or allow more memory for QLever during startup

[Tool]
SPARQL execution failed:
Tried to allocate 48.5 GB, but only 12 GB were available. Clear the cache or allow more memory for QLever during startup

[Tool]
SPARQL execution failed:
Tried to allocate 48.5 GB, but only 12 GB were available. Clear the cache or allow more memory for QLever during startup

[Tool] Stopped generation process


PREFIX uniparc: <http://purl.uniprot.org/uniparc/>
SELECT ?predicate ?object WHERE {
  uniparc:UPI000012A0AD ?predicate ?object
}

Got 211 rows and 2 columns, showing the first 5 and last 5 rows below:
| predicate                     | object                                            |
| ----------------------------- | ------------------------------------------------- |
| length (up:length)            | 508 (xsd:int)                                     |
| MD5 checksum (up:md5Checksum) | 8599b15580dbb2f39b50b691226f9f66                  |
| member of (up:memberOf)       | <http://purl.uniprot.org/uniref/UniRef100_P19235> |
| member of (up:memberOf)       | <http://purl.uniprot.org/uniref/UniRef50_P19235>  |
| member of (up:memberOf)       | <http://purl.uniprot.org/uniref/UniRef90_P19235>  |
| ...                           | ...                                               |
| see also (rdfs:seeAlso)       | <http://purl.uniprot.org/pirsf/PIRSF001959>       |
| see also (rdfs:seeAlso)       | <http://purl.uniprot.org/prosite/PS01352>         |
| see also (rdfs:seeAlso)       | <http://purl.uniprot.org/prosite/PS50853>         |
| see also (rdfs:seeAlso)       | <http://purl.uniprot.org/smart/SM00060>           |
| see also (rdfs:seeAlso)       | <http://purl.uniprot.org/supfam/SSF49265>         |

Here is a SPARQL query that retrieves all predicates and objects directly associated with the UniParc accession UPI000012A0AD:

```sparql
SELECT ?predicate ?object WHERE {
  uniparc:UPI000012A0AD ?predicate ?object
}
```

This query will return all predicates and their corresponding objects for the given UniParc accession.

[System]
You are a question answering assistant. Your job is to generate a SPARQL query to answer a given user question.

You have access to the following knowledge graphs:
uniprot at https://qlever.cs.uni-freiburg.de/api/uniprot

You can use the following SPARQL prefixes implicitly in all functions:
ECO: <http://purl.obolibrary.org/obo/ECO_
annotation: <http://purl.uniprot.org/annotation/
bibo: <http://purl.org/ontology/bibo/
busco: <http://busco.ezlab.org/schema#
chebi: <http://purl.obolibrary.org/obo/CHEBI_
citation: <http://purl.uniprot.org/citations/
cito: <http://purl.org/spar/cito/
dcat: <http://www.w3.org/ns/dcat#
dcmit: <http://purl.org/dc/dcmitype/
dcterms: <http://purl.org/dc/terms/
disease: <http://purl.uniprot.org/diseases/
embl-cds: <http://purl.uniprot.org/embl-cds/
ensembl: <http://rdf.ebi.ac.uk/resource/ensembl/
enzyme: <http://purl.uniprot.org/enzyme/
faldo: <http://biohackathon.org/resource/faldo#
foaf: <http://xmlns.com/foaf/0.1/
go: <http://purl.obolibrary.org/obo/GO_
hs: <https://hamap.expasy.org/rdf/vocab#
isoform: <http://purl.uniprot.org/isoforms/
keywords: <http://purl.uniprot.org/keywords/
location: <http://purl.uniprot.org/locations/
obo: <http://purl.obolibrary.org/obo/
oboInOwl: <http://www.geneontology.org/formats/oboInOwl#
owl: <http://www.w3.org/2002/07/owl#
patent: <http://purl.uniprot.org/EPO/
pav: <http://purl.org/pav/
position: <http://purl.uniprot.org/position/
prism: <http://prismstandard.org/namespaces/basic/2.0/
pubmed: <http://purl.uniprot.org/pubmed/
range: <http://purl.uniprot.org/range/
rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#
rdfs: <http://www.w3.org/2000/01/rdf-schema#
rh: <http://rdf.rhea-db.org/
schema: <http://schema.org/
sd: <http://www.w3.org/ns/sparql-service-description#
sh: <http://www.w3.org/ns/shacl#
skos: <http://www.w3.org/2004/02/skos/core#
sp: <http://spinrdf.org/sp#
ssmRegion: <http://purl.uniprot.org/signatureSequenceMatch/
stato: <http://purl.obolibrary.org/obo/STATO_
taxon: <http://purl.uniprot.org/taxonomy/
tissue: <http://purl.uniprot.org/tissues/
uniparc: <http://purl.uniprot.org/uniparc/
uniprot: <http://purl.uniprot.org/uniprot/
up: <http://purl.uniprot.org/core/
voag: <http://voag.linkedmodel.org/schema/voag#
void: <http://rdfs.org/ns/void#
xsd: <http://www.w3.org/2001/XMLSchema#
dc: <http://purl.org/dc/elements/1.1/
prov: <http://www.w3.org/ns/prov#
geo: <http://www.opengis.net/ont/geosparql#
geosparql: <http://www.opengis.net/ont/geosparql#
gn: <http://www.geonames.org/ontology#
bd: <http://www.bigdata.com/rdf#
hint: <http://www.bigdata.com/queryHints#
wikibase: <http://wikiba.se/ontology#
qb: <http://purl.org/linked-data/cube#

You should follow a step-by-step approach to generate the SPARQL query:
1. Determine possible entities and properties implied by the user question.
2. Use the functions to search for entities and properties in the knowledge graphs. Where applicable, constrain the searches with already identified entities and properties.
3. Gradually build up the SPARQL query using the identified entities and properties. Start with simple queries and add more complexity as needed. Use the execute function to get feedback on intermediate queries. You can go back and forth between knowledge graph searches and SPARQL query executions to refine the query.
4. Use the answer or cancel function to finalize your answer and stop the generation process.

Additional rules:
1. Explain your thought process before and after each step and function call.
2. Do not assume or make up any entities or properties without verifying them with the knowledge graphs and functions.
3. The SPARQL query should always return the actual identifiers / IRIs of the items in its result. It additionally may return labels or other human-readable information, but they are optional and should be put within optional clauses unless explicitly requested by the user.
4. Do not stop early if there are still obvious improvements to be made to the SPARQL query. For example, keep refining your SPARQL query if its result contains irrelevant items or is missing items you expected.
5. Do not perform additional computation (e.g. filtering, sorting, calculations) on the result of the SPARQL query to determine the answer. All computation should be done solely within SPARQL.
6. For questions with a "True" or "False" answer the SPARQL query should be an ASK query.
7. Do not use 'SERVICE wikibase:label { bd:serviceParam wikibase:language ...' in SPARQL queries. It is not SPARQL standard and unsupported by the used QLever SPARQL endpoints. Use rdfs:label or similar properties to get labels instead.

[User] What are the predicates and objects directly associated with the UniParc accession UPI000012A0AD?

[Assistant]
To answer this question, I need to find all triples where the subject is the UniParc accession UPI000012A0AD. In UniProt RDF, UniParc accessions are typically represented as IRIs like uniparc:UPI000012A0AD.

I will list all triples with subject uniparc:UPI000012A0AD to see the predicates and objects directly associated with it.

[Tool]
Got 211 rows and 3 columns, showing the first 10 rows below:
| subject               | property                      | object                                                              |
| --------------------- | ----------------------------- | ------------------------------------------------------------------- |
| uniparc:UPI000012A0AD | type (rdf:type)               | Sequence (up:Sequence)                                              |
| uniparc:UPI000012A0AD | see also (rdfs:seeAlso)       | <http://purl.uniprot.org/cdd/cd00063>                               |
| uniparc:UPI000012A0AD | sequence for (up:sequenceFor) | <http://purl.uniprot.org/EMBL_CON/EAW84205>                         |
| uniparc:UPI000012A0AD | label (rdfs:label)            | Erythropoietin receptor                                             |
| uniparc:UPI000012A0AD | member of (up:memberOf)       | <http://purl.uniprot.org/uniref/UniRef100_P19235>                   |
| uniparc:UPI000012A0AD | value (rdf:value)             | MDHLGASLWPQVGSLCLLLAGAAWAPPPNLPD...QGGLSDGPYSNPYENSLIPAAEPLPPSYVACS |
| uniparc:UPI000012A0AD | MD5 checksum (up:md5Checksum) | 8599b15580dbb2f39b50b691226f9f66                                    |
| uniparc:UPI000012A0AD | length (up:length)            | 508 (xsd:int)                                                       |
| uniparc:UPI000012A0AD | type (rdf:type)               | Sequence (up:Sequence)                                              |
| uniparc:UPI000012A0AD | see also (rdfs:seeAlso)       | <http://purl.uniprot.org/funfam/G3DSA:2.60.40.10:FF:001041>         |
| ...                   | ...                           | ...                                                                 |

[Assistant]
Here is a SPARQL query that retrieves all predicates and objects directly associated with the UniParc accession UPI000012A0AD:

```sparql
SELECT ?predicate ?object WHERE {
  uniparc:UPI000012A0AD ?predicate ?object
}
```

This query will return all predicates and their corresponding objects for the given UniParc accession.

[User]
Feedback (status=done):
The SPARQL query correctly retrieves all predicates and objects directly associated with the UniParc accession UPI000012A0AD. It returns the IRIs of the predicates and objects as required, and does not include any unnecessary computation or filtering. The answer is complete and matches the user's request.