Add .gitignore entries and commit reference cache files

- Ignore .umap_cache/ and *.bak backup files
- Add PubMed/DOI reference cache files for reproducibility

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: realmarcin

.gitignore

@@ -52,6 +52,12 @@ tmp/
 # Media cache (CultureMech/MediaIngredientMech data - can be regenerated)
 media_cache/
 
+# UMAP cache (embedding cache - can be regenerated)
+.umap_cache/
+
+# Backup files
+*.bak
+
 # Reports (generated files - can be regenerated)
 reports/*.csv
 reports/*.txt

references_cache/PMID_15545431.md

@@ -0,0 +1,70 @@
+---
+reference_id: PMID:15545431
+title: "Clostridium straminisolvens sp. nov., a moderately thermophilic, aerotolerant and cellulolytic bacterium isolated from a cellulose-degrading bacterial community."
+authors:
+- Kato S
+- Haruta S
+- Cui ZJ
+- Ishii M
+- Yokota A
+- Igarashi Y
+journal: Int J Syst Evol Microbiol
+year: '2004'
+doi: 10.1099/ijs.0.63148-0
+keywords:
+- Anaerobiosis
+- Cellulose/metabolism
+- "Clostridium/classification, cytology, isolation & purification, physiology"
+- "DNA, Bacterial/chemistry, isolation & purification"
+- "DNA, Ribosomal/chemistry, isolation & purification"
+- "Genes, rRNA"
+- Hydrogen-Ion Concentration
+- Molecular Sequence Data
+- Movement
+- Oxygen/toxicity
+- Phylogeny
+- "RNA, Bacterial/genetics"
+- "RNA, Ribosomal, 16S/genetics"
+- "Sequence Analysis, DNA"
+- "Spores, Bacterial/cytology"
+- Temperature
+content_type: abstract_only
+---
+
+# Clostridium straminisolvens sp. nov., a moderately thermophilic, aerotolerant and cellulolytic bacterium isolated from a cellulose-degrading bacterial community.
+**Authors:** Kato S, Haruta S, Cui ZJ, Ishii M, Yokota A, Igarashi Y
+**Journal:** Int J Syst Evol Microbiol (2004)
+**DOI:** [10.1099/ijs.0.63148-0](https://doi.org/10.1099/ijs.0.63148-0)
+
+## Content
+
+1. Int J Syst Evol Microbiol. 2004 Nov;54(Pt 6):2043-2047. doi: 
+10.1099/ijs.0.63148-0.
+
+Clostridium straminisolvens sp. nov., a moderately thermophilic, aerotolerant 
+and cellulolytic bacterium isolated from a cellulose-degrading bacterial 
+community.
+
+Kato S(1), Haruta S(1), Cui ZJ(1), Ishii M(1), Yokota A(2), Igarashi Y(1).
+
+Author information:
+(1)Department of Biotechnology, Graduate School of Agricultural and Life 
+Sciences, University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan.
+(2)Laboratory of Bioresources, Institute of Molecular and Cellular Biosciences, 
+University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan.
+
+A novel anaerobic, thermophilic and cellulolytic bacterium (strain CSK1(T)) was 
+isolated from a cellulose-degrading bacterial community. On the basis of 16S 
+rRNA gene sequence similarity, strain CSK1(T) was mapped to cluster III of the 
+genus Clostridium. Strain CSK1(T) is closely related to Clostridium thermocellum 
+(96.2 %) and Clostridium aldrichii (95.1 %). Strain CSK1(T) is a non-motile, 
+spore-forming, straight or slightly curved rod. The optimum temperature and 
+initial pH for its growth and cellulose degradation are 50-55 degrees C and pH 
+7.5. Strain CSK1(T) grew under a gas phase containing up to 4 % O(2). 
+Phylogenetic and phenotypic analyses support the differentiation of strain 
+CSK1(T) from its closest relatives. Strain CSK1(T) therefore represents a novel 
+species, for which the name Clostridium straminisolvens sp. nov. is proposed, 
+with CSK1(T) (=DSM 16021(T)=IAM 15070(T)) as the type strain.
+
+DOI: 10.1099/ijs.0.63148-0
+PMID: 15545431 [Indexed for MEDLINE]