publication not found when the publication exist

[JannahS]

Hi there,

I've recently discovered your tool, and it seems suitable for my purpose.

However, when I tried to query my gene, using both uniprot ID or gene symbol, no pubmed results were returned.

My query would be "TAF9 AND neurodegenerative".

Here's my input dataframe, taf9:

	UniProtID	GeneID	IDType	TaxID	Keyword	KeywordInTitleOnly
1	D6RIV9	TAF9	Accession	9606	neurodegenerative	no

And I ran

result <- omixLitMiner(taf9)

Same result when I used "Gene" as IDType.

When I tried using EUtilsSummary, three publications matched my queries:

TAF9 <- EUtilsSummary("TAF9 AND neurodegenerative",
                      type = "esearch",
                      db = "pubmed",
                      datetype = "pdat",
                      retmax = 1000,
                      mindate = 2000,
                      maxdate = 2021)


# fetch data
fetch_TAF9 <- EUtilsGet(TAF9, type = "efetch", db = "pubmed")


# Create data frame
abstracts_TAF9 <- data.frame(title = fetch_TAF9@ArticleTitle,
                        abstract = fetch_TAF9@AbstractText,
                        journal = fetch_TAF9@Title,
                        DOI = fetch_TAF9@PMID,
                        year = fetch_TAF9@YearPubmed)


if (length(abstracts_TAF9$title)==0) {
  cat("No publications found")
} else {
    kable(abstracts_TAF9, "html")  %>% kable_paper(c("striped", "hover") ,font_size = 12) %>% 
scroll_box(width = "100%", height = "400px")
}

title	abstract	journal	DOI	year
Nonallele specific silencing of ataxin-7 improves disease phenotypes in a mouse model of SCA7.	Spinocerebellar ataxia type 7 (SCA7) is a late-onset neurodegenerative disease characterized by ataxia and vision loss with no effective treatments in the clinic. The most striking feature is the degeneration of Purkinje neurons of the cerebellum caused by the presence of polyglutamine-expanded ataxin-7. Ataxin-7 is part of a transcriptional complex, and, in the setting of mutant ataxin-7, there is misregulation of target genes. Here, we designed RNAi sequences to reduce the expression of both wildtype and mutant ataxin-7 to test if reducing ataxin-7 in Purkinje cells is both tolerated and beneficial in an animal model of SCA7. We observed sustained reduction of both wildtype and mutant ataxin-7 as well as a significant improvement of ataxia phenotypes. Furthermore, we observed a reduction in cerebellar molecular layer thinning and nuclear inclusions, a hallmark of SCA7. In addition, we observed recovery of cerebellar transcripts whose expression is disrupted in the presence of mutant ataxin-7. These data demonstrate that reduction of both wildtype and mutant ataxin-7 by RNAi is well tolerated, and contrary to what may be expected from reducing a component of the Spt-Taf9-Gcn5 acetyltransferase complex, is efficacious in the SCA7 mouse.	NA	24930601	2014
Both normal and polyglutamine- expanded ataxin-7 are components of TFTC-type GCN5 histone acetyltransferase- containing complexes.	SCA7 (spinocerebellar ataxia type 7) is a neurodegenerative disorder caused by a CAG repeat expansion in the SCA7 gene that leads to elongation of a polyglutamine tract in ataxin-7, a protein of unknown function. Sgf73, a putative yeast orthologue of ataxin-7, has been identified as a new component of the yeast SAGA (Spt/Ada/Gcn5 acetyltransferase) multisubunit complex, a co-activator required for the transcription of a subset of RNA polymerase II-dependent genes. We show here that ataxin-7 is an integral component of mammalian SAGA-like complexes, i.e. the TFTC [TBP (TATA-binding protein)-free TAF (TBP-associated factor) complex] and the STAGA (SPT3/TAF9/GCN5 acetyltransferase) complex. In agreement with this, immunoprecipitation of ataxin-7 retained a histone acetyltransferase activity characteristic of TFTC-like complexes. Moreover, polyglutamine expansion in ataxin-7 did not affect its incorporation into TFTCs/STAGA complexes purified from cells from a SCA7 patient. We demonstrate here that ataxin-7 is the human orthologue of a the yeast SAGA Sgf73 subunit, and is a bona fide subunit of human TFTC-like transcriptional complexes.	NA	16626296	2006
Ataxin-7 is a subunit of GCN5 histone acetyltransferase-containing complexes.	Spinocerebellar ataxia type 7 (SCA7) is a neurodegenerative disorder caused by a CAG repeat expansion in the SCA7 gene leading to elongation of a polyglutamine tract in ataxin-7, a protein of unknown function. A putative ataxin-7 yeast orthologue (SGF73) has been identified recently as a new component of the SAGA (Spt/Ada/Gcn5 acetylase) multisubunit complex, a coactivator required for transcription of a subset of RNA polymerase II-dependent genes. We show here that ataxin-7 is an integral component of the mammalian SAGA-like complexes, the TATA-binding protein-free TAF-containing complex (TFTC) and the SPT3/TAF9/GCN5 acetyltransferase complex (STAGA). In agreement, immunoprecipitation of ataxin-7 retained a histone acetyltransferase activity, characteristic for TFTC-like complexes. We further identified a minimal domain in ataxin-7 that is required for interaction with TFTC/STAGA subunits and is conserved highly through evolution, allowing the identification of a SCA7 gene family. We showed that this domain contains a conserved Cys(3)His motif that binds zinc, forming a new zinc-binding domain. Finally, polyglutamine expansion in ataxin-7 did not affect its incorporation into TFTC/STAGA complexes purified from SCA7 patient cells. We demonstrate here that ataxin-7 is the human orthologue of the yeast SAGA SGF73 subunit and is a bona fide subunit of the human TFTC-like transcriptional complexes.	NA	15115762	2004

Would you be able to advice why your tool did not detect the three publications?