Add data files with SQLite files properly configured for Git LFS

.gitattributes

@@ -25,6 +25,7 @@
 *.pth filter=lfs diff=lfs merge=lfs -text
 *.rar filter=lfs diff=lfs merge=lfs -text
 *.safetensors filter=lfs diff=lfs merge=lfs -text
+*.sqlite filter=lfs diff=lfs merge=lfs -text
 saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 *.tar.* filter=lfs diff=lfs merge=lfs -text
 *.tar filter=lfs diff=lfs merge=lfs -text

README.md

@@ -44,6 +44,84 @@ The datasets in this repository store datasets used by our MCP server which enab
 
 Contributions to this dataset collection are welcome. Please follow standard Git LFS practices when adding new biological data files.
 
+## Using the Data in Your Project
+
+To use the datasets in this repository with your Python projects, you can leverage the `huggingface-hub` library for easy downloading and caching of specific files, and `uv` for managing your project dependencies.
+
+### 1. Setting up your environment with `uv`
+
+First, ensure you have `uv` installed. If not, you can install it following the official `uv` installation guide (e.g., `pip install uv` or other methods recommended by astral.sh).
+
+Then, create and activate a virtual environment for your project:
+```bash
+uv venv my_project_env  # Creates a virtual environment named my_project_env
+source my_project_env/bin/activate # On Linux/macOS
+# my_project_env\Scripts\activate # On Windows
+```
+
+Install the `huggingface-hub` library into your activated environment:
+```bash
+uv pip install huggingface-hub
+```
+If you plan to work with common data formats, you might also want to install libraries like `pandas`:
+```bash
+uv pip install pandas
+```
+
+### 2. Accessing data files with `huggingface-hub`
+
+You can download individual files from this Hugging Face Dataset repository using the `hf_hub_download` function from the `huggingface-hub` library. This function handles the download and caches the file locally for future use.
+
+**Example:**
+
+Let's assume you want to download a specific data file, for instance, `hagr/anage_data.csv` from this repository.
+
+```python
+from huggingface_hub import hf_hub_download
+import os # Optional: for constructing paths
+
+# Define the repository ID and the file path within the repository
+repo_id = "longevity-genie/bio-mcp-data"  # This is the Hugging Face Hub ID for this dataset
+# IMPORTANT: Replace "hagr/anage_data.csv" with the actual path to a file in this repository.
+# You can browse the files on the Hugging Face Hub page for this dataset to find correct paths.
+file_to_download = "hagr/anage_data.csv"
+
+try:
+    # Download the file
+    downloaded_file_path = hf_hub_download(
+        repo_id=repo_id,
+        filename=file_to_download,
+        repo_type="dataset"  # Crucial for dataset repositories
+    )
+    
+    print(f"File '{file_to_download}' downloaded successfully to: {downloaded_file_path}")
+
+    # Now you can use the downloaded_file_path to load and process the data.
+    # For example, if it's a CSV file and you have pandas installed:
+    import pandas as pd
+    try:
+        data_frame = pd.read_csv(downloaded_file_path)
+        print("Successfully loaded data into pandas DataFrame:")
+        print(data_frame.head())
+    except Exception as e_pandas:
+        print(f"Could not load CSV with pandas: {e_pandas}")
+
+except Exception as e:
+    print(f"An error occurred while trying to download '{file_to_download}': {e}")
+    print(f"Please ensure the file path is correct and the file exists in the repository '{repo_id}'.")
+    print("You can check available files at: https://huggingface.co/datasets/longevity-genie/bio-mcp-data/tree/main")
+
+```
+
+**Explanation:**
+
+-   **`repo_id`**: This is the identifier of the dataset on Hugging Face Hub (`longevity-genie/bio-mcp-data`).
+-   **`filename`**: This is the relative path to the file *within* the repository (e.g., `data/some_file.fasta`, `annotations/genes.gff`). You need to replace `"hagr/anage_data.csv"` with the actual path to a file you intend to use.
+-   **`repo_type="dataset"`**: This tells `huggingface-hub` that you are targeting a dataset repository.
+-   The `hf_hub_download` function returns the local path to the downloaded (and cached) file. You can then use this path with any Python library that can read files (like `pandas` for CSVs, `BioPython` for sequence files, etc.).
+
+This method is efficient as it only downloads the files you specifically request and utilizes local caching, saving time and bandwidth on subsequent runs.
+
 ## License
 
 This project is licensed under the MIT License - see the license information above for details.

hagr/anage_data.sqlite

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:576fcd5c85f59904fe8934fd4901893158a1f1a2b5e3089cd5ae7cb2fad9c28b
+size 802816

just-dna-seq/Species.csv

@@ -0,0 +1,343 @@
+"Common name","Scientific name","Taxon ID","Ensembl Assembly","Accession","Genebuild Method","Variation database","Regulation database"
+"Abingdon island giant tortoise","Chelonoidis abingdonii","106734","ASM359739v1","GCA_003597395.1","Full genebuild","-","-"
+"African ostrich","Struthio camelus australis","441894","ASM69896v1","GCA_000698965.1","Full genebuild","-","-"
+"Agassiz's desert tortoise","Gopherus agassizii","38772","ASM289641v1","GCA_002896415.1","Full genebuild","-","-"
+"Algerian mouse","Mus spretus","10096","SPRET_EiJ_v1","GCA_001624865.1","External annotation import","-","Y"
+"Alpaca","Vicugna pacos","30538","vicPac1","-","Projection build","-","-"
+"Alpine marmot","Marmota marmota marmota","9994","marMar2.1","GCA_001458135.1","Full genebuild","-","-"
+"Amazon molly","Poecilia formosa","48698","Poecilia_formosa-5.1.2","GCA_000485575.1","Full genebuild","-","-"
+"American beaver","Castor canadensis","51338","C.can_genome_v1.0","GCA_001984765.1","Full genebuild","-","-"
+"American bison","Bison bison bison","43346","Bison_UMD1.0","GCA_000754665.1","Full genebuild","Y","-"
+"American black bear","Ursus americanus","9643","ASM334442v1","GCA_003344425.1","Full genebuild","-","-"
+"American mink","Neovison vison","452646","NNQGG.v01","GCA_900108605.1","Full genebuild","Y","-"
+"Angola colobus","Colobus angolensis palliatus","336983","Cang.pa_1.0","GCA_000951035.1","Full genebuild","-","Y"
+"Arabian camel","Camelus dromedarius","9838","CamDro2","GCA_000803125.2","Full genebuild","-","-"
+"Arctic ground squirrel","Urocitellus parryii","9999","ASM342692v1","GCA_003426925.1","Full genebuild","-","-"
+"Argentine black and white tegu","Salvator merianae","96440","HLtupMer3","GCA_003586115.1","Full genebuild","-","-"
+"Armadillo","Dasypus novemcinctus","9361","Dasnov3.0","GCA_000208655.2","Mixed strategy build","-","-"
+"Asian bonytongue","Scleropages formosus","113540","fSclFor1.1","GCA_900964775.1","Full genebuild","-","-"
+"Asiatic black bear","Ursus thibetanus thibetanus","441215","ASM966005v1","GCA_009660055.1","Full genebuild","-","-"
+"Atlantic cod","Gadus morhua","8049","gadMor3.0","GCA_902167405.1","Full genebuild","-","-"
+"Atlantic cod - Celtic sea","Gadus morhua","8049","gadMor_Celtic","GCA_010882105.1","Full genebuild","-","-"
+"Atlantic herring ","Clupea harengus","7950","Ch_v2.0.2v2","GCA_900700415.2","Full genebuild","-","-"
+"Atlantic salmon","Salmo salar","8030","Ssal_v3.1","GCA_905237065.2","Full genebuild","Y","Y"
+"Atlantic salmon - European origin ALTA","Salmo salar","8030","Ssal_ALTA","GCA_931346935.2","Full genebuild","-","-"
+"Atlantic salmon - North American Atlantic Salmon","Salmo salar","8030","USDA_NASsal_1.1","GCA_021399835.1","Full genebuild","-","-"
+"Atlantic salmon - North American origin Brian","Salmo salar","8030","Ssal_Brian_v1.0","GCA_923944775.1","Full genebuild","-","-"
+"Australian saltwater crocodile","Crocodylus porosus","8502","CroPor_comp1","GCA_001723895.1","Full genebuild","-","-"
+"Ballan wrasse","Labrus bergylta","56723","BallGen_V1","GCA_900080235.1","Full genebuild","-","-"
+"Barramundi perch","Lates calcarifer","8187","ASB_HGAPassembly_v1","GCA_900066035.1","Full genebuild","-","-"
+"Beluga whale","Delphinapterus leucas","9749","ASM228892v3","GCA_002288925.3","Full genebuild","-","-"
+"Bengalese finch","Lonchura striata domestica","299123","LonStrDom1","GCA_002197715.1","Full genebuild","-","-"
+"Bicolor damselfish","Stegastes partitus","144197","Stegastes_partitus-1.0.2","GCA_000690725.1","Full genebuild","-","-"
+"Black snub-nosed monkey","Rhinopithecus bieti","61621","ASM169854v1","GCA_001698545.1","Full genebuild","-","Y"
+"Blind barbel","Sinocyclocheilus anshuiensis","1608454","SAMN03320099.WGS_v1.1","GCA_001515605.1","Full genebuild","-","-"
+"Blue tilapia","Oreochromis aureus","47969","ZZ_aureus","GCA_013358895.1","Full genebuild","-","-"
+"Blue tit","Cyanistes caeruleus","156563","cyaCae2","GCA_002901205.1","Full genebuild","-","-"
+"Blue whale","Balaenoptera musculus","9771","mBalMus1.v2","GCA_009873245.2","Full genebuild","-","-"
+"Blue-crowned manakin","Lepidothrix coronata","321398","Lepidothrix_coronata-1.0","GCA_001604755.1","Full genebuild","-","-"
+"Blue-ringed sea krait","Laticauda laticaudata","8630","latLat_1.0","GCA_004320025.1","Full genebuild","-","-"
+"Blunt-snouted clingfish","Gouania willdenowi","441366","fGouWil2.1","GCA_900634775.1","Full genebuild","-","-"
+"Bolivian squirrel monkey","Saimiri boliviensis boliviensis","39432","SaiBol1.0","GCA_000235385.1","Full genebuild","-","Y"
+"Bonobo","Pan paniscus","9597","panpan1.1","GCA_000258655.2","Full genebuild","-","Y"
+"Brazilian guinea pig","Cavia aperea","37548","CavAp1.0","GCA_000688575.1","Full genebuild","-","-"
+"Brown trout","Salmo trutta","8032","fSalTru1.1","GCA_901001165.1","Full genebuild","-","-"
+"Budgerigar","Melopsittacus undulatus","13146","bMelUnd1.mat.Z","GCA_012275295.1","Full genebuild","-","-"
+"Burrowing owl","Athene cunicularia","194338","athCun1","GCA_003259725.1","Full genebuild","-","-"
+"Burton's mouthbrooder","Haplochromis burtoni","8153","AstBur1.0","GCA_000239415.1","Full genebuild","-","-"
+"Bushbaby","Otolemur garnettii","30611","OtoGar3","GCA_000181295.3","Full genebuild","-","-"
+"C.intestinalis","Ciona intestinalis","7719","KH","GCA_000224145.1","Full genebuild","Y","Y"
+"C.savignyi","Ciona savignyi","51511","CSAV 2.0","-","Full genebuild","-","-"
+"Caenorhabditis elegans (Nematode, N2)","Caenorhabditis elegans","6239","WBcel235","GCA_000002985.3","Import","-","Y"
+"California sea lion","Zalophus californianus","9704","mZalCal1.pri","GCA_009762305.1","Full genebuild","-","-"
+"Canada lynx","Lynx canadensis","61383","mLynCan4_v1.p","GCA_007474595.1","Full genebuild","-","-"
+"Cat","Felis catus","9685","Felis_catus_9.0","GCA_000181335.4","Full genebuild","Y","Y"
+"Central bearded dragon","Pogona vitticeps","103695","pvi1.1","GCA_900067755.1","Full genebuild","-","-"
+"Chacoan peccary","Catagonus wagneri","51154","CatWag_v2_BIUU_UCD","GCA_004024745.2","Full genebuild","-","-"
+"Channel bull blenny","Cottoperca gobio","56716","fCotGob3.1","GCA_900634415.1","Full genebuild","-","-"
+"Channel catfish","Ictalurus punctatus","7998","ASM400665v3","GCA_004006655.3","Full genebuild","-","Y"
+"Chicken","Gallus gallus","9031","bGalGal1.mat.broiler.GRCg7b","GCA_016699485.1","Full genebuild","Y","Y"
+"Chicken (Red Jungle fowl)","Gallus gallus","9031","GRCg6a","GCA_000002315.5","Full genebuild","Y","Y"
+"Chicken (paternal White leghorn layer)","Gallus gallus","9031","bGalGal1.pat.whiteleghornlayer.GRCg7w","GCA_016700215.2","Full genebuild","-","-"
+"Chilean tinamou","Nothoprocta perdicaria","30464","notPer1","GCA_003342845.1","Full genebuild","-","-"
+"Chimpanzee","Pan troglodytes","9598","Pan_tro_3.0","GCA_000001515.5","Full genebuild","Y","Y"
+"Chinese hamster CHOK1GS","Cricetulus griseus","10029","CHOK1GS_HDv1","GCA_900186095.1","Full genebuild","-","Y"
+"Chinese hamster CriGri","Cricetulus griseus","10029","CriGri_1.0","GCA_000223135.1","Full genebuild","-","Y"
+"Chinese hamster PICR","Cricetulus griseus","10029","CriGri-PICRH-1.0","GCA_003668045.2","Full genebuild","-","-"
+"Chinese medaka","Oryzias sinensis","183150","ASM858656v1","GCA_008586565.1","Full genebuild","-","-"
+"Chinese softshell turtle","Pelodiscus sinensis","13735","PelSin_1.0","GCA_000230535.1","Mixed strategy build","-","-"
+"Chinook salmon","Oncorhynchus tshawytscha","74940","Otsh_v2.0","GCA_018296145.1","Full genebuild","-","-"
+"Climbing perch","Anabas testudineus","64144","fAnaTes1.3","GCA_900324465.3","Full genebuild","-","-"
+"Clown anemonefish","Amphiprion ocellaris","80972","ASM2253959v1","GCA_022539595.1","Full genebuild","-","-"
+"Coelacanth","Latimeria chalumnae","7897","LatCha1","GCA_000225785.1","Full genebuild","-","-"
+"Coho salmon","Oncorhynchus kisutch","8019","Okis_V2","GCA_002021735.2","Full genebuild","-","-"
+"Collared flycatcher","Ficedula albicollis","59894","FicAlb1.5","GCA_000247815.2","Full genebuild","Y","-"
+"Common canary","Serinus canaria","9135","SCA1","GCA_000534875.1","Full genebuild","-","-"
+"Common carp","Cyprinus carpio carpio","630221","Cypcar_WagV4.0","GCA_905221575.1","Full genebuild","-","Y"
+"Common carp german mirror","Cyprinus carpio","7962","German_Mirror_carp_1.0","GCA_004011555.1","Full genebuild","-","-"
+"Common carp hebao red","Cyprinus carpio","7962","Hebao_red_carp_1.0","GCA_004011595.1","Full genebuild","-","-"
+"Common carp huanghe","Cyprinus carpio","7962","Hunaghe_carp_2.0","GCA_004011575.1","Full genebuild","-","-"
+"Common kestrel","Falco tinnunculus","100819","FalTin1.0","GCA_010332995.1","Full genebuild","-","-"
+"Common snapping turtle","Chelydra serpentina","8475","Chelydra_serpentina-1.0","GCA_007922165.1","Full genebuild","-","-"
+"Common wall lizard","Podarcis muralis","64176","PodMur_1.0","GCA_004329235.1","Full genebuild","-","-"
+"Common wombat","Vombatus ursinus","29139","bare-nosed_wombat_genome_assembly","GCA_900497805.2","Full genebuild","-","-"
+"Coquerel's sifaka","Propithecus coquereli","379532","Pcoq_1.0","GCA_000956105.1","Full genebuild","-","Y"
+"Cow","Bos taurus","9913","ARS-UCD1.3","GCA_002263795.3","Full genebuild","Y","Y"
+"Crab-eating macaque","Macaca fascicularis","9541","Macaca_fascicularis_6.0","GCA_011100615.1","Full genebuild","Y","-"
+"Damara mole rat","Fukomys damarensis","885580","DMR_v1.0","GCA_000743615.1","Full genebuild","-","-"
+"Dark-eyed junco","Junco hyemalis","40217","ASM382977v1","GCA_003829775.1","Full genebuild","-","-"
+"Daurian ground squirrel","Spermophilus dauricus","99837","ASM240643v1","GCA_002406435.1","Full genebuild","-","-"
+"Degu","Octodon degus","10160","OctDeg1.0","GCA_000260255.1","Full genebuild","-","-"
+"Denticle herring","Denticeps clupeoides","299321","fDenClu1.2","GCA_900700375.2","Full genebuild","-","-"
+"Dingo","Canis lupus dingo","286419","ASM325472v1","GCA_003254725.1","Full genebuild","-","-"
+"Dog","Canis lupus familiaris","9615","ROS_Cfam_1.0","GCA_014441545.1","Full genebuild","Y","Y"
+"Dog - Basenji","Canis lupus familiaris","9615","Basenji_breed-1.1","GCA_004886185.1","Full genebuild","-","Y"
+"Dog - Boxer","Canis lupus familiaris","9615","Dog10K_Boxer_Tasha","GCA_000002285.4","Full genebuild","Y","Y"
+"Dog - German Shepherd","Canis lupus familiaris","9615","UU_Cfam_GSD_1.0","GCA_011100685.1","Full genebuild","-","-"
+"Dog - Great Dane","Canis lupus familiaris","9615","UMICH_Zoey_3.1","GCA_005444595.1","Full genebuild","-","Y"
+"Dolphin","Tursiops truncatus","9739","turTru1","-","Projection build","-","-"
+"Domestic yak","Bos grunniens","30521","LU_Bosgru_v3.0","GCA_005887515.1","Full genebuild","Y","-"
+"Donkey","Equus asinus","9793","ASM1607732v2","GCA_016077325.2","Full genebuild","-","-"
+"Drill","Mandrillus leucophaeus","9568","Mleu.le_1.0","GCA_000951045.1","Full genebuild","-","Y"
+"Drosophila melanogaster (Fruit fly)","Drosophila melanogaster","7227","BDGP6.46","GCA_000001215.4","Import","Y","Y"
+"Duck","Anas platyrhynchos platyrhynchos","8840","CAU_duck1.0","GCA_002743455.1","Full genebuild","-","Y"
+"Eastern brown snake","Pseudonaja textilis","8673","EBS10Xv2-PRI","GCA_900518735.1","Full genebuild","-","-"
+"Eastern buzzard","Buteo japonicus","224669","ButJap1.0","GCA_010312235.1","Full genebuild","-","-"
+"Eastern happy","Astatotilapia calliptera","8154","fAstCal1.3","GCA_900246225.5","Full genebuild","-","-"
+"Eastern spot-billed duck","Anas zonorhyncha","75864","ASM222487v1","GCA_002224875.1","Full genebuild","-","-"
+"Electric eel","Electrophorus electricus","8005","fEleEle1.pri","GCA_013358815.1","Full genebuild","-","-"
+"Elephant","Loxodonta africana","9785","Loxafr3.0","GCA_000001905.1","Full genebuild","-","-"
+"Elephant shark","Callorhinchus milii","7868","Callorhinchus_milii-6.1.3","GCA_000165045.2","Full genebuild","-","-"
+"Emu","Dromaius novaehollandiae","8790","droNov1","GCA_003342905.1","Full genebuild","-","-"
+"Eurasian eagle-owl","Bubo bubo","30461","BubBub1.0","GCA_010303855.1","Full genebuild","-","-"
+"Eurasian red squirrel","Sciurus vulgaris","55149","mSciVul1.1","GCA_902686455.1","Full genebuild","-","-"
+"Eurasian sparrowhawk","Accipiter nisus","211598","Accipiter_nisus_ver1.0","GCA_004320145.1","Full genebuild","-","-"
+"European seabass","Dicentrarchus labrax","13489","dlabrax2021","GCA_905237075.1","Full genebuild","Y","Y"
+"Ferret","Mustela putorius furo","9669","MusPutFur1.0","GCA_000215625.1","Mixed strategy build","-","-"
+"Fugu","Takifugu rubripes","31033","fTakRub1.2","GCA_901000725.2","Full genebuild","-","-"
+"Gelada","Theropithecus gelada","9565","Tgel_1.0","GCA_003255815.1","Full genebuild","-","Y"
+"Giant panda","Ailuropoda melanoleuca","9646","ASM200744v2","GCA_002007445.2","Full genebuild","-","-"
+"Gibbon","Nomascus leucogenys","61853","Nleu_3.0","GCA_000146795.3","Full genebuild","Y","Y"
+"Gilthead seabream","Sparus aurata","8175","fSpaAur1.1","GCA_900880675.1","Full genebuild","-","-"
+"Goat","Capra hircus","9925","ARS1","GCA_001704415.1","Full genebuild","Y","Y"
+"Goat (black bengal)","Capra hircus","9925","CVASU_BBG_1.0","GCA_004361675.1","Full genebuild","-","-"
+"Goat - Saanen Dairy","Capra hircus","9925","Saanen_v1","GCA_015443085.1","Full genebuild","-","-"
+"Goat - Xinong Saanen Dairy","Capra hircus","9925","ASM2665220v1","GCA_026652205.1","Full genebuild","-","-"
+"Golden Hamster","Mesocricetus auratus","10036","MesAur1.0","GCA_000349665.1","Full genebuild","-","Y"
+"Golden eagle","Aquila chrysaetos chrysaetos","223781","bAquChr1.2","GCA_900496995.2","Full genebuild","-","-"
+"Golden pheasant","Chrysolophus pictus","9089","Chrysolophus_pictus_GenomeV1.0","GCA_003413605.1","Full genebuild","-","-"
+"Golden snub-nosed monkey","Rhinopithecus roxellana","61622","Rrox_v1","GCA_000769185.1","Full genebuild","-","Y"
+"Golden-collared manakin","Manacus vitellinus","328815","ASM171598v2","GCA_001715985.2","Full genebuild","-","-"
+"Golden-line barbel","Sinocyclocheilus grahami","75366","SAMN03320097.WGS_v1.1","GCA_001515645.1","Full genebuild","-","-"
+"Goldfish","Carassius auratus","7957","ASM336829v1","GCA_003368295.1","Full genebuild","-","-"
+"Goodes thornscrub tortoise","Gopherus evgoodei","1825980","rGopEvg1_v1.p","GCA_007399415.1","Full genebuild","-","-"
+"Gorilla","Gorilla gorilla gorilla","9595","gorGor4","GCA_000151905.3","Full genebuild","-","Y"
+"Gouldian finch","Erythrura gouldiae","44316","GouldianFinch","GCA_003676055.1","Full genebuild","-","-"
+"Great Tit","Parus major","9157","Parus_major1.1","GCA_001522545.2","Full genebuild","Y","-"
+"Great spotted kiwi","Apteryx haastii","8823","aptHaa1","GCA_003342985.1","Full genebuild","-","-"
+"Greater amberjack","Seriola dumerili","41447","Sdu_1.0","GCA_002260705.1","Full genebuild","Y","-"
+"Greater bamboo lemur","Prolemur simus","1328070","Prosim_1.0","GCA_003258685.1","Full genebuild","-","Y"
+"Greater horseshoe bat","Rhinolophus ferrumequinum","59479","mRhiFer1_v1.p","GCA_004115265.2","Full genebuild","-","-"
+"Green anole","Anolis carolinensis","28377","AnoCar2.0v2","GCA_000090745.2","Full genebuild","-","-"
+"Guinea Pig","Cavia porcellus","10141","Cavpor3.0","GCA_000151735.1","Full genebuild","Y","Y"
+"Guppy","Poecilia reticulata","8081","Guppy_female_1.0_MT","GCA_000633615.2","Full genebuild","-","-"
+"Hagfish","Eptatretus burgeri","7764","Eburgeri_3.2","GCA_900186335.2","Full genebuild","-","-"
+"Hedgehog","Erinaceus europaeus","9365","eriEur1","-","Projection build","-","-"
+"Helmeted guineafowl","Numida meleagris","8996","NumMel1.0","GCA_002078875.2","Full genebuild","-","-"
+"Horned golden-line barbel","Sinocyclocheilus rhinocerous","307959","SAMN03320098_v1.1","GCA_001515625.1","Full genebuild","-","-"
+"Horse","Equus caballus","9796","EquCab3.0","GCA_002863925.1","Full genebuild","Y","Y"
+"Huchen","Hucho hucho","62062","ASM331708v1","GCA_003317085.1","Full genebuild","-","-"
+"Human","Homo sapiens","9606","GRCh38.p14","GCA_000001405.29","Full genebuild","Y","Y"
+"Hybrid - Bos Indicus","Bos indicus x Bos taurus","30522","UOA_Brahman_1","GCA_003369695.2","Full genebuild","-","-"
+"Hybrid - Bos Taurus","Bos indicus x Bos taurus","30522","UOA_Angus_1","GCA_003369685.2","Full genebuild","-","-"
+"Hyrax","Procavia capensis","9813","proCap1","-","Projection build","-","-"
+"Indian cobra","Naja naja","35670","Nana_v5","GCA_009733165.1","Full genebuild","-","-"
+"Indian glassy fish","Parambassis ranga","210632","fParRan2.2","GCA_900634625.2","Full genebuild","-","-"
+"Indian medaka","Oryzias melastigma","30732","Om_v0.7.RACA","GCA_002922805.1","Full genebuild","-","-"
+"Indian peafowl","Pavo cristatus","9049","AIIM_Pcri_1.0","GCA_005519975.1","Full genebuild","-","-"
+"Japanese medaka HNI","Oryzias latipes","8090","ASM223471v1","GCA_002234715.1","Full genebuild","-","-"
+"Japanese medaka HSOK","Oryzias latipes","8090","ASM223469v1","GCA_002234695.1","Full genebuild","-","-"
+"Japanese medaka HdrR","Oryzias latipes","8090","ASM223467v1","GCA_002234675.1","Full genebuild","-","-"
+"Japanese quail","Coturnix japonica","93934","Coturnix_japonica_2.0","GCA_001577835.1","Full genebuild","Y","-"
+"Javanese ricefish","Oryzias javanicus","123683","OJAV_1.1","GCA_003999625.1","Full genebuild","-","-"
+"Jewelled blenny","Salarias fasciatus","181472","fSalaFa1.1","GCA_902148845.1","Full genebuild","-","-"
+"Kakapo","Strigops habroptila","2489341","bStrHab1_v1.p","GCA_004027225.1","Full genebuild","-","-"
+"Kangaroo rat","Dipodomys ordii","10020","Dord_2.0","GCA_000151885.2","Full genebuild","-","-"
+"Koala","Phascolarctos cinereus","38626","phaCin_unsw_v4.1","GCA_002099425.1","Full genebuild","-","-"
+"Komodo dragon","Varanus komodoensis","61221","ASM479886v1","GCA_004798865.1","Full genebuild","-","-"
+"Lamprey","Petromyzon marinus","7757","Pmarinus_7.0","-","Full genebuild","-","-"
+"Large yellow croaker","Larimichthys crocea","215358","L_crocea_2.0","GCA_000972845.2","Full genebuild","-","-"
+"Leishan spiny toad","Leptobrachium leishanense","445787","ASM966780v1","GCA_009667805.1","Full genebuild","-","-"
+"Leopard","Panthera pardus","9691","PanPar1.0","GCA_001857705.1","Full genebuild","-","-"
+"Lesser Egyptian jerboa","Jaculus jaculus","51337","JacJac1.0","GCA_000280705.1","Full genebuild","-","-"
+"Lesser hedgehog tenrec","Echinops telfairi","9371","TENREC","-","Projection build","-","-"
+"Lion","Panthera leo","9689","PanLeo1.0","GCA_008795835.1","Full genebuild","-","-"
+"Little spotted kiwi","Apteryx owenii","8824","aptOwe1","GCA_003342965.1","Full genebuild","-","-"
+"Live sharksucker","Echeneis naucrates","173247","fEcheNa1.1","GCA_900963305.1","Full genebuild","-","-"
+"Long-tailed chinchilla","Chinchilla lanigera","34839","ChiLan1.0","GCA_000276665.1","Full genebuild","-","-"
+"Lumpfish","Cyclopterus lumpus","8103","fCycLum1.pri","GCA_009769545.1","Full genebuild","-","-"
+"Lyretail cichlid","Neolamprologus brichardi","32507","NeoBri1.0","GCA_000239395.1","Full genebuild","-","-"
+"Ma's night monkey","Aotus nancymaae","37293","Anan_2.0","GCA_000952055.2","Full genebuild","-","Y"
+"Macaque","Macaca mulatta","9544","Mmul_10","GCA_003339765.3","Full genebuild","Y","Y"
+"Mainland tiger snake","Notechis scutatus","8663","TS10Xv2-PRI","GCA_900518725.1","Full genebuild","-","-"
+"Makobe Island cichlid","Pundamilia nyererei","303518","PunNye1.0","GCA_000239375.1","Full genebuild","-","-"
+"Mallard","Anas platyrhynchos","8839","ASM874695v1","GCA_008746955.1","Full genebuild","Y","-"
+"Mangrove rivulus","Kryptolebias marmoratus","37003","ASM164957v1","GCA_001649575.1","Full genebuild","-","-"
+"Medium ground-finch","Geospiza fortis","48883","GeoFor_1.0","GCA_000277835.1","Full genebuild","-","-"
+"Meerkat","Suricata suricatta","37032","meerkat_22Aug2017_6uvM2_HiC","GCA_006229205.1","Full genebuild","-","-"
+"Megabat","Pteropus vampyrus","132908","pteVam1","-","Projection build","-","-"
+"Mexican tetra","Astyanax mexicanus","7994","Astyanax_mexicanus-2.0","GCA_000372685.2","Full genebuild","-","-"
+"Microbat","Myotis lucifugus","59463","Myoluc2.0","GCA_000147115.1","Full genebuild","-","-"
+"Midas cichlid","Amphilophus citrinellus","61819","Midas_v5","GCA_000751415.1","Full genebuild","-","-"
+"Mongolian gerbil","Meriones unguiculatus","10047","MunDraft-v1.0","GCA_002204375.1","Full genebuild","-","-"
+"Monterrey platyfish","Xiphophorus couchianus","32473","Xiphophorus_couchianus-4.0.1","GCA_001444195.1","Full genebuild","-","-"
+"Mouse","Mus musculus","10090","GRCm39","GCA_000001635.9","Full genebuild","Y","Y"
+"Mouse 129S1/SvImJ","Mus musculus","10090","129S1_SvImJ_v1","GCA_001624185.1","External annotation import","-","Y"
+"Mouse A/J","Mus musculus","10090","A_J_v1","GCA_001624215.1","External annotation import","-","Y"
+"Mouse AKR/J","Mus musculus","10090","AKR_J_v1","GCA_001624295.1","External annotation import","-","Y"
+"Mouse BALB/cJ","Mus musculus","10090","BALB_cJ_v1","GCA_001632525.1","External annotation import","-","Y"
+"Mouse C3H/HeJ","Mus musculus","10090","C3H_HeJ_v1","GCA_001632575.1","External annotation import","-","Y"
+"Mouse C57BL/6NJ","Mus musculus","10090","C57BL_6NJ_v1","GCA_001632555.1","External annotation import","-","Y"
+"Mouse CAST/EiJ","Mus musculus castaneus","10091","CAST_EiJ_v1","GCA_001624445.1","External annotation import","-","Y"
+"Mouse CBA/J","Mus musculus","10090","CBA_J_v1","GCA_001624475.1","External annotation import","-","Y"
+"Mouse DBA/2J","Mus musculus","10090","DBA_2J_v1","GCA_001624505.1","External annotation import","-","Y"
+"Mouse FVB/NJ","Mus musculus","10090","FVB_NJ_v1","GCA_001624535.1","External annotation import","-","Y"
+"Mouse LP/J","Mus musculus","10090","LP_J_v1","GCA_001632615.1","External annotation import","-","Y"
+"Mouse Lemur","Microcebus murinus","30608","Mmur_3.0","GCA_000165445.3","Full genebuild","-","Y"
+"Mouse NOD/ShiLtJ","Mus musculus","10090","NOD_ShiLtJ_v1","GCA_001624675.1","External annotation import","-","Y"
+"Mouse NZO/HlLtJ","Mus musculus","10090","NZO_HlLtJ_v1","GCA_001624745.1","External annotation import","-","Y"
+"Mouse PWK/PhJ","Mus musculus musculus","39442","PWK_PhJ_v1","GCA_001624775.1","External annotation import","-","Y"
+"Mouse WSB/EiJ","Mus musculus domesticus","10092","WSB_EiJ_v1","GCA_001624835.1","External annotation import","-","Y"
+"Mummichog","Fundulus heteroclitus","8078","Fundulus_heteroclitus-3.0.2","GCA_000826765.1","Full genebuild","-","Y"
+"Muscovy Duck (domestic type)","Cairina moschata domestica","1240228","CaiMos1.0","GCA_009194515.1","Full genebuild","-","-"
+"Naked mole-rat female","Heterocephalus glaber","10181","Naked_mole-rat_maternal","GCA_944319715.1","Full genebuild","-","-"
+"Naked mole-rat male","Heterocephalus glaber","10181","Naked_mole-rat_paternal","GCA_944319725.1","Full genebuild","-","-"
+"Narwhal","Monodon monoceros","40151","NGI_Narwhal_1","GCA_005190385.2","Full genebuild","-","-"
+"New Caledonian crow","Corvus moneduloides","1196302","bCorMon1.pri","GCA_009650955.1","Full genebuild","-","-"
+"Nile tilapia","Oreochromis niloticus","8128","O_niloticus_UMD_NMBU","GCA_001858045.3","Full genebuild","Y","-"
+"Northern American deer mouse","Peromyscus maniculatus bairdii","230844","HU_Pman_2.1","GCA_003704035.1","Full genebuild","-","-"
+"Northern pike","Esox lucius","8010","fEsoLuc1.pri","GCA_011004845.1","Full genebuild","-","-"
+"Northern spotted owl","Strix occidentalis caurina","311401","Soccid_v01","GCA_002372975.1","Full genebuild","-","-"
+"Ocean sunfish","Mola mola","94237","ASM169857v1","GCA_001698575.1","Full genebuild","-","-"
+"Okarito brown kiwi","Apteryx rowi","308060","aptRow1","GCA_003343035.1","Full genebuild","-","-"
+"Olive baboon","Papio anubis","9555","Panubis1.0","GCA_008728515.1","Full genebuild","-","Y"
+"Opossum","Monodelphis domestica","13616","ASM229v1","GCA_000002295.1","Full genebuild","Y","-"
+"Orange clownfish","Amphiprion percula","161767","Nemo_v1","GCA_003047355.1","Full genebuild","-","-"
+"Orbiculate cardinalfish","Sphaeramia orbicularis","375764","fSphaOr1.1","GCA_902148855.1","Full genebuild","-","-"
+"Oriental scops-owl","Otus sunia","257818","OtuSun1.0","GCA_010365825.1","Full genebuild","-","-"
+"Pachon cavefish","Astyanax mexicanus","7994","Astyanax_mexicanus-1.0.2","GCA_004802775.1","Full genebuild","-","-"
+"Painted turtle","Chrysemys picta bellii","8478","Chrysemys_picta_bellii-3.0.3","GCA_000241765.2","Full genebuild","-","-"
+"Panamanian white-faced capuchin","Cebus imitator","2715852","Cebus_imitator-1.0","GCA_001604975.1","Full genebuild","-","-"
+"P. kingsleyae","Paramormyrops kingsleyae","1676925","PKINGS_0.1","GCA_002872115.1","Full genebuild","-","-"
+"P. magnuspinnatus","Periophthalmus magnuspinnatus","409849","PM.fa","GCA_000787105.1","Full genebuild","-","-"
+"Pig","Sus scrofa","9823","Sscrofa11.1","GCA_000003025.6","Full genebuild","Y","Y"
+"Pig - Bama miniature","Sus scrofa","9823","ASM764409v1","GCA_007644095.1","Full genebuild","-","-"
+"Pig - Bamei","Sus scrofa","9823","Bamei_pig_v1","GCA_001700235.1","Full genebuild","-","-"
+"Pig - Berkshire","Sus scrofa","9823","Berkshire_pig_v1","GCA_001700575.1","Full genebuild","-","-"
+"Pig - Duroc","Sus scrofa","9823","Ninghe_Sus_1","GCA_015776825.1","Full genebuild","-","-"
+"Pig - Hampshire","Sus scrofa","9823","Hampshire_pig_v1","GCA_001700165.1","Full genebuild","-","-"
+"Pig - Jinhua","Sus scrofa","9823","Jinhua_pig_v1","GCA_001700295.1","Full genebuild","-","-"
+"Pig - Landrace","Sus scrofa","9823","Landrace_pig_v1","GCA_001700215.1","Full genebuild","-","-"
+"Pig - Largewhite","Sus scrofa","9823","Large_White_v1","GCA_001700135.1","Full genebuild","-","-"
+"Pig - Meishan","Sus scrofa","9823","Meishan_pig_v1","GCA_001700195.1","Full genebuild","-","-"
+"Pig - Meishan (GCA_017957985.1)","Sus scrofa domesticus","9825","ASM1795798v1","GCA_017957985.1","Full genebuild","-","-"
+"Pig - NIHS-2020","Sus scrofa","9823","ASM1855540v1","GCA_018555405.1","Full genebuild","-","-"
+"Pig - Ningxiang","Sus scrofa domesticus","9825","ASM2056790v1","GCA_020567905.1","Full genebuild","-","-"
+"Pig - Ossabaw miniature","Sus scrofa","9823","ASM2471841v1","GCA_024718415.1","Full genebuild","-","-"
+"Pig - PB115","Sus scrofa","9823","CAU-K","GCA_019290145.1","Full genebuild","-","-"
+"Pig - Pietrain","Sus scrofa","9823","Pietrain_pig_v1","GCA_001700255.1","Full genebuild","-","-"
+"Pig - Rongchang","Sus scrofa","9823","Rongchang_pig_v1","GCA_001700155.1","Full genebuild","-","-"
+"Pig - Tibetan","Sus scrofa","9823","Tibetan_Pig_v2","GCA_000472085.2","Full genebuild","-","-"
+"Pig - Wuzhishan","Sus scrofa","9823","minipig_v1.0","GCA_000325925.2","Full genebuild","-","-"
+"Pig - euw1 (european wild boar)","Sus scrofa","9823","ASM2165605v1","GCA_021656055.1","Full genebuild","-","-"
+"Pig USMARC","Sus scrofa","9823","USMARCv1.0","GCA_002844635.1","Full genebuild","-","-"
+"Pig-tailed macaque","Macaca nemestrina","9545","Mnem_1.0","GCA_000956065.1","Full genebuild","-","Y"
+"Pika","Ochotona princeps","9978","OchPri2.0-Ens","-","Projection build","-","-"
+"Pike-perch","Sander lucioperca","283035","SLUC_FBN_1","GCA_008315115.1","Full genebuild","Y","-"
+"Pinecone soldierfish","Myripristis murdjan","586833","fMyrMur1.1","GCA_902150065.1","Full genebuild","-","-"
+"Pink-footed goose","Anser brachyrhynchus","132585","ASM259213v1","GCA_002592135.1","Full genebuild","-","-"
+"Platyfish","Xiphophorus maculatus","8083","X_maculatus-5.0-male","GCA_002775205.2","Full genebuild","-","-"
+"Platypus","Ornithorhynchus anatinus","9258","mOrnAna1.p.v1","GCA_004115215.2","Full genebuild","Y","Y"
+"Polar bear","Ursus maritimus","29073","UrsMar_1.0","GCA_000687225.1","Full genebuild","-","-"
+"Prairie vole","Microtus ochrogaster","79684","MicOch1.0","GCA_000317375.1","Full genebuild","Y","-"
+"Rabbit","Oryctolagus cuniculus","9986","OryCun2.0","GCA_000003625.1","Full genebuild","Y","Y"
+"Rainbow trout","Oncorhynchus mykiss","8022","USDA_OmykA_1.1","GCA_013265735.3","Full genebuild","Y","Y"
+"Rat","Rattus norvegicus","10116","mRatBN7.2","GCA_015227675.2","Full genebuild","Y","Y"
+"Rat - SHR/Utx RGD_8142385","Rattus norvegicus","10116","UTH_Rnor_SHR_Utx","GCA_023515785.1","Full genebuild","-","-"
+"Rat - SHRSP/BbbUtx","Rattus norvegicus","10116","UTH_Rnor_SHRSP_BbbUtx_1.0","GCA_021556685.1","Full genebuild","-","-"
+"Rat - WKY/Bbb RGD_1581635","Rattus norvegicus","10116","UTH_Rnor_WKY_Bbb_1.0","GCA_023515805.1","Full genebuild","-","-"
+"Red fox","Vulpes vulpes","9627","VulVul2.2","GCA_003160815.1","Full genebuild","-","-"
+"Red-bellied piranha","Pygocentrus nattereri","42514","fPygNat1.pri","GCA_015220715.1","Full genebuild","-","-"
+"Reedfish","Erpetoichthys calabaricus","27687","fErpCal1.1","GCA_900747795.2","Full genebuild","-","-"
+"Ring-necked pheasant","Phasianus colchicus","9054","ASM414374v1","GCA_004143745.1","Full genebuild","-","-"
+"Round goby","Neogobius melanostomus","47308","RGoby_Basel_V2","GCA_007210695.1","Full genebuild","-","-"
+"Ruff","Calidris pugnax","198806","ASM143184v1","GCA_001431845.1","Full genebuild","-","-"
+"Rufous-capped babbler","Cyanoderma ruficeps","181631","ASM869450v1","GCA_008694505.1","Full genebuild","-","-"
+"Ryukyu mouse","Mus caroli","10089","CAROLI_EIJ_v1.1","GCA_900094665.2","External annotation import","-","-"
+"Saccharomyces cerevisiae","Saccharomyces cerevisiae S288c","559292","R64-1-1","GCA_000146045.2","Import","Y","Y"
+"Sailfin molly","Poecilia latipinna","48699","P_latipinna-1.0","GCA_001443285.1","Full genebuild","-","-"
+"Sheep","Ovis aries","9940","ARS-UI_Ramb_v2.0","GCA_016772045.1","Full genebuild","Y","-"
+"Sheep (texel)","Ovis aries","9940","Oar_v3.1","GCA_000298735.1","Mixed strategy build","Y","-"
+"Sheep - Chinese merino","Ovis aries","9940","ASM2243282v1","GCA_022432825.1","Full genebuild","-","-"
+"Sheep - East friesian","Ovis aries","9940","NWAFU_Friesian_1.0","GCA_018804185.1","Full genebuild","-","-"
+"Sheep - Hu","Ovis aries","9940","ASM1117029v1","GCA_011170295.1","Full genebuild","-","-"
+"Sheep - Kermani","Ovis aries","9940","ASM2243283v1","GCA_022432835.1","Full genebuild","-","-"
+"Sheep - Polled Dorset","Ovis aries","9940","ASM2241691v1","GCA_022416915.1","Full genebuild","-","-"
+"Sheep - Qiaoke","Ovis aries","9940","ASM2241668v1","GCA_022416685.1","Full genebuild","-","-"
+"Sheep - Romanov","Ovis aries","9940","ASM2422217v1","GCA_024222175.1","Full genebuild","-","-"
+"Sheep - White dorper","Ovis aries","9940","ASM2241669v1","GCA_022416695.1","Full genebuild","-","-"
+"Sheepshead minnow","Cyprinodon variegatus","28743","C_variegatus-1.0","GCA_000732505.1","Full genebuild","-","Y"
+"Shortfin molly","Poecilia mexicana","48701","P_mexicana-1.0","GCA_001443325.1","Full genebuild","-","-"
+"Shrew","Sorex araneus","42254","sorAra1","-","Projection build","-","-"
+"Shrew mouse","Mus pahari","10093","PAHARI_EIJ_v1.1","GCA_900095145.2","External annotation import","-","-"
+"Siamese fighting fish","Betta splendens","158456","fBetSpl5.2","GCA_900634795.2","Full genebuild","-","-"
+"Siberian musk deer","Moschus moschiferus","68415","MosMos_v2_BIUU_UCD","GCA_004024705.2","Full genebuild","-","-"
+"Silver-eye","Zosterops lateralis melanops","1220523","ASM128173v1","GCA_001281735.1","Full genebuild","-","-"
+"Sloth","Choloepus hoffmanni","9358","choHof1","-","Projection build","-","-"
+"Small tree finch","Camarhynchus parvulus","87175","Camarhynchus_parvulus_V1.1","GCA_902806625.1","Full genebuild","-","-"
+"Sooty mangabey","Cercocebus atys","9531","Caty_1.0","GCA_000955945.1","Full genebuild","-","Y"
+"Sperm whale","Physeter catodon","9755","ASM283717v2","GCA_002837175.2","Full genebuild","-","-"
+"Spiny chromis","Acanthochromis polyacanthus","80966","ASM210954v1","GCA_002109545.1","Full genebuild","-","-"
+"Spoon-billed sandpiper","Calidris pygmaea","425635","ASM369795v1","GCA_003697955.1","Full genebuild","-","-"
+"Spotted gar","Lepisosteus oculatus","7918","LepOcu1","GCA_000242695.1","Full genebuild","-","-"
+"Squirrel","Ictidomys tridecemlineatus","43179","SpeTri2.0","GCA_000236235.1","Full genebuild","-","-"
+"Steppe mouse","Mus spicilegus","10103","MUSP714","GCA_003336285.1","Full genebuild","-","-"
+"Stickleback","Gasterosteus aculeatus aculeatus","481459","GAculeatus_UGA_version5","GCA_016920845.1","Full genebuild","-","-"
+"Sumatran orangutan","Pongo abelii","9601","Susie_PABv2","GCA_002880775.3","Full genebuild","Y","-"
+"Superb fairywren","Malurus cyaneus samueli","2593467","mCya_1.0","GCA_009741485.1","Full genebuild","-","-"
+"Swainson's thrush","Catharus ustulatus","91951","bCatUst1.pri","GCA_009819885.1","Full genebuild","-","-"
+"Swamp eel","Monopterus albus","43700","M_albus_1.0","GCA_001952655.1","Full genebuild","-","-"
+"Swan goose","Anser cygnoides","8845","GooseV1.0","GCA_002166845.1","Full genebuild","-","-"
+"Tarsier","Carlito syrichta","1868482","Tarsius_syrichta-2.0.1","GCA_000164805.2","Full genebuild","-","Y"
+"Tasmanian devil","Sarcophilus harrisii","9305","mSarHar1.11","GCA_902635505.1","Full genebuild","-","-"
+"Tetraodon","Tetraodon nigroviridis","99883","TETRAODON 8.0","-","Full genebuild","Y","-"
+"Three-spined sticklebacki - Freshwater BOT","Gasterosteus aculeatus","69293","BOT","GCA_006229185.1","Full genebuild","-","-"
+"Three-spined sticklebacki - Marine BAM","Gasterosteus aculeatus","69293","BAM","GCA_006232265.1","Full genebuild","-","-"
+"Three-spined sticklebacki - Marine SYL","Gasterosteus aculeatus","69293","SYL","GCA_006232285.1","Full genebuild","-","-"
+"Three-toed box turtle","Terrapene carolina triunguis","2587831","T_m_triunguis-2.0","GCA_002925995.2","Full genebuild","-","-"
+"Tiger","Panthera tigris altaica","74533","PanTig1.0","GCA_000464555.1","Full genebuild","-","-"
+"Tiger tail seahorse","Hippocampus comes","109280","H_comes_QL1_v1","GCA_001891065.1","Full genebuild","-","-"
+"Tongue sole","Cynoglossus semilaevis","244447","Cse_v1.0","GCA_000523025.1","Full genebuild","-","-"
+"Tree Shrew","Tupaia belangeri","37347","tupBel1","-","Projection build","-","-"
+"Tropical clawed frog","Xenopus tropicalis","8364","UCB_Xtro_10.0","GCA_000004195.4","Full genebuild","-","-"
+"Tuatara","Sphenodon punctatus","8508","ASM311381v1","GCA_003113815.1","Full genebuild","-","-"
+"Turbot","Scophthalmus maximus","52904","ASM1334776v1","GCA_013347765.1","Full genebuild","-","Y"
+"Turkey","Meleagris gallopavo","9103","Turkey_5.1","GCA_000146605.4","Full genebuild","Y","-"
+"Turquoise killifish","Nothobranchius furzeri","105023","Nfu_20140520","GCA_001465895.2","Full genebuild","-","-"
+"Ugandan red Colobus","Piliocolobus tephrosceles","591936","ASM277652v2","GCA_002776525.2","Full genebuild","-","Y"
+"Upper Galilee mountains blind mole rat","Nannospalax galili","1026970","S.galili_v1.0","GCA_000622305.1","Full genebuild","-","Y"
+"Vaquita","Phocoena sinus","42100","mPhoSin1.pri","GCA_008692025.1","Full genebuild","-","-"
+"Vervet-AGM","Chlorocebus sabaeus","60711","ChlSab1.1","GCA_000409795.2","Full genebuild","Y","-"
+"Wallaby","Notamacropus eugenii","9315","Meug_1.0","GCA_000004035.1","Projection build","-","-"
+"West African mud turtle","Pelusios castaneus","367368","Pelusios_castaneus-1.0","GCA_007922175.1","Full genebuild","-","-"
+"Western mosquitofish","Gambusia affinis","33528","ASM309773v1","GCA_003097735.1","Full genebuild","-","-"
+"White-throated sparrow","Zonotrichia albicollis","44394","Zonotrichia_albicollis-1.0.1","GCA_000385455.1","Full genebuild","-","-"
+"White-tufted-ear marmoset","Callithrix jacchus","9483","mCalJac1.pat.X","GCA_011100555.1","Full genebuild","Y","Y"
+"Wild yak","Bos mutus","72004","BosGru_v2.0","GCA_000298355.1","Full genebuild","-","-"
+"Yarkand deer","Cervus hanglu yarkandensis","84702","CEY_v1","GCA_010411085.1","Full genebuild","-","-"
+"Yellow-billed parrot","Amazona collaria","241587","ASM394721v1","GCA_003947215.1","Full genebuild","-","-"
+"Yellowtail amberjack","Seriola lalandi dorsalis","1841481","Sedor1","GCA_002814215.1","Full genebuild","-","-"
+"Zebra finch","Taeniopygia guttata","59729","bTaeGut1_v1.p","GCA_003957565.2","Full genebuild","Y","-"
+"Zebra mbuna","Maylandia zebra","106582","M_zebra_UMD2a","GCA_000238955.5","Full genebuild","-","-"
+"Zebrafish","Danio rerio","7955","GRCz11","GCA_000002035.4","Full genebuild","Y","Y"
+"Zig-zag eel","Mastacembelus armatus","205130","fMasArm1.2","GCA_900324485.2","Full genebuild","-","-"

just-dna-seq/coronary.sqlite

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just-dna-seq/lipid_metabolism.sqlite

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just-dna-seq/longevitymap.sqlite

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just-dna-seq/thrombophilia.sqlite

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opengenes/open_genes.sqlite

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opengenes/prompt.txt

@@ -0,0 +1,877 @@
+# OpenGenes Database Assistant
+
+You are a knowledgeable biology and longevity research assistant with access to the OpenGenes database containing aging and lifespan research data.
+
+## Your Task
+Answer questions about genes, aging, lifespan, and longevity research by querying the database using the `db_query(sql:str)` tool.
+
+## Key Query Guidelines
+
+### 1. Multi-Value Fields (CRITICAL)
+Some columns contain comma-separated values representing multiple tags per row. For these fields, ALWAYS use LIKE queries with wildcards:
+
+**Multi-value columns:**
+- `gene_hallmarks.hallmarks of aging` - contains multiple aging hallmarks
+- `lifespan_change.intervention_deteriorates` - contains multiple biological processes that deteriorate  
+- `lifespan_change.intervention_improves` - contains multiple biological processes that improve
+
+**Example queries:**
+```sql
+-- Find genes with specific hallmark
+WHERE "hallmarks of aging" LIKE '%stem cell exhaustion%'
+
+-- Find interventions affecting cardiovascular system
+WHERE intervention_deteriorates LIKE '%cardiovascular system%'
+```
+
+### 2. Enumeration Matching
+For columns with enumerations (listed below), match user input to the closest enumeration value before querying.
+
+### 3. Gene Symbol Queries
+Use the `HGNC` column for gene symbols (standard gene names like TP53, FOXO3, etc.).
+
+### 4. Result Ordering for Lifespan Effects
+When querying lifespan effects, order results by the magnitude of effect to show the most relevant results first:
+
+**For lifespan extension queries:**
+- Order by largest lifespan increase first (highest `lifespan_percent_change_mean` or `lifespan_percent_change_median`)
+- Use `ORDER BY lifespan_percent_change_mean DESC` or similar
+
+**For lifespan reduction queries:**
+- Order by largest lifespan decrease first (lowest/most negative `lifespan_percent_change_mean`)
+- Use `ORDER BY lifespan_percent_change_mean ASC` or similar
+
+**Example ordering queries:**
+```sql
+-- Genes that extend lifespan, ordered by greatest extension
+SELECT HGNC, effect_on_lifespan, lifespan_percent_change_mean
+FROM lifespan_change 
+WHERE effect_on_lifespan = 'increases lifespan'
+ORDER BY lifespan_percent_change_mean DESC;
+
+-- Genes that reduce lifespan, ordered by greatest reduction
+SELECT HGNC, effect_on_lifespan, lifespan_percent_change_mean
+FROM lifespan_change 
+WHERE effect_on_lifespan = 'decreases lifespan'
+ORDER BY lifespan_percent_change_mean ASC;
+```
+
+## Database Structure
+
+The database contains 4 main tables:
+
+### lifespan_change
+**Purpose:** Experimental data on how gene modifications affect lifespan
+**Key columns:** HGNC, model_organism, effect_on_lifespan, intervention methods, biological effects
+**Use for:** Questions about gene effects on lifespan, experimental conditions, organism studies
+
+### gene_criteria  
+**Purpose:** Aging-related criteria that genes meet
+**Key columns:** HGNC, criteria
+**Use for:** Questions about why genes are considered aging-related
+
+### gene_hallmarks
+**Purpose:** Links genes to hallmarks of aging
+**Key columns:** HGNC, hallmarks of aging (multi-value)
+**Use for:** Questions about which aging hallmarks genes are involved in
+
+### longevity_associations
+**Purpose:** Population genetics data on gene variants and longevity
+**Key columns:** HGNC, polymorphism data, ethnicity, study type
+**Use for:** Questions about genetic variants associated with longevity
+
+## Quick Reference: Available Tags
+
+### Hallmarks of Aging (for gene_hallmarks table)
+- nuclear DNA instability
+- telomere attrition  
+- alterations in histone modifications
+- chromatin remodeling
+- transcriptional alterations
+- alterations in DNA methylation
+- degradation of proteolytic systems
+- TOR pathway dysregulation
+- INS/IGF-1 pathway dysregulation
+- AMPK pathway dysregulation
+- SIRT pathway dysregulation
+- impairment of the mitochondrial integrity and biogenesis
+- mitochondrial DNA instability
+- accumulation of reactive oxygen species
+- senescent cells accumulation
+- stem cell exhaustion
+- sterile inflammation
+- intercellular communication impairment
+- changes in the extracellular matrix structure
+- impairment of proteins folding and stability
+- nuclear architecture impairment
+- disabled macroautophagy
+
+### Biological Processes/Systems (for intervention effects)
+- cardiovascular system
+- nervous system
+- immune function
+- muscle, bone, skin, liver
+- renal function, reproductive function
+- cognitive function, eyesight, hair/coat
+- body composition
+- glucose metabolism, lipid metabolism, cholesterol metabolism
+- insulin sensitivity
+- oxidation/antioxidant function, mitochondrial function
+- DNA metabolism, carcinogenesis, apoptosis
+- senescence, inflammation, stress responce
+- autophagy, proliferation, locomotor function
+- tissue regeneration, stem and progenitor cells
+- blood, proteostasis, angiogenesis, metabolism
+- endocrine system, intercellular matrix
+- building and protection of telomeres
+- cytoskeleton organization, nucleus structure
+- skin and the intestine epithelial barriers function
+- calcium homeostasis, proteolysis
+
+---
+
+## Detailed Table Schemas
+
+### lifespan_change Table
+```sql
+CREATE TABLE "lifespan_change" (
+  "HGNC" TEXT, -- gene symbol
+  "model_organism" TEXT, -- organism used for the experiment
+  "sex" TEXT, -- sex of an organism used for the experiment
+  "line" TEXT, -- line of an organism used for the experiment
+  "effect_on_lifespan" TEXT, -- direction of change in lifespan (increased, decreased, no change)
+  "control_cohort_size" REAL, -- number of animals in the control cohort
+  "experiment_cohort_size" REAL, -- number of animals in the experiment
+  "quantity_of_animals_in_cage_or_container" REAL, -- quantity of animals in the cage or container
+  "containment_t_celsius_from" REAL, -- temperature from which the experiment was conducted
+  "containment_t_celsius_to" TEXT, -- temperature to which the experiment was conducted
+  "diet" TEXT, -- diet of an organism used for the experiment
+  "target_gene_expression_change" REAL, -- target gene expression change
+  "control_lifespan_min" REAL, -- minimum lifespan of the control
+  "control_lifespan_mean" REAL, -- mean lifespan of the control
+  "control_lifespan_median" REAL, -- median lifespan of the control
+  "control_lifespan_max" REAL, -- maximum lifespan of the control
+  "experiment_lifespan_min" REAL, -- minimum lifespan of the experiment
+  "experiment_lifespan_mean" REAL, -- mean lifespan of the experiment
+  "experiment_lifespan_median" REAL, -- median lifespan of the experiment
+  "experiment_lifespan_max" REAL, -- maximum lifespan of the experiment
+  "lifespan_time_unit" TEXT, -- time unit of the lifespan
+  "lifespan_percent_change_min" REAL, -- minimum percent change in lifespan
+  "significance_min" INTEGER, -- significance of the minimum lifespan change
+  "lifespan_percent_change_mean" REAL, -- mean percent change in lifespan
+  "significance_mean" INTEGER, -- significance of the mean lifespan change
+  "lifespan_percent_change_median" REAL, -- median percent change in lifespan
+  "significance_median" INTEGER, -- significance of the median lifespan change
+  "lifespan_percent_change_max" REAL, -- percent of the change of maximum lifespan
+  "significance_max" INTEGER, -- significance of the maximum lifespan change
+  "intervention_deteriorates" TEXT, -- processes/organs/systems in which was observed deterioration (multi-value)
+  "intervention_improves" TEXT, -- processes/organs/systems in which was observed improvement (multi-value)
+  "main_effect_on_lifespan" TEXT, -- direction of change in gene activity (gain of function, loss of function)
+  "intervention_way" TEXT, -- particular method of gene activity changing
+  "intervention_method" TEXT, -- the tissue in which the gene was affected, if tissue-specific
+  "genotype" TEXT, -- genotype of an organism used for the experiment
+  "tissue" TEXT, -- tissue of an organism used for the experiment
+  "tissue_specific_promoter" TEXT,
+  "induction_by_drug_withdrawal" INTEGER,
+  "drug" TEXT,
+  "treatment_start" TEXT,
+  "treatment_end" TEXT,
+  "doi" TEXT, -- doi of the article
+  "pmid" REAL -- pmid of the article
+)
+```
+
+## Column Enumerations
+
+For columns with fixed sets of values, match user input to these exact enumeration values:
+
+### lifespan_change Table Enumerations
+Column: model_organism
+Enumerations:
+  - mouse
+  - roundworm Caenorhabditis elegans
+  - fly Drosophila melanogaster
+  - rabbit
+  - rat
+  - acyrthosiphon pisum
+  - yeasts 
+  - fish Nothobranchius furzeri
+  - fungus Podospora anserina
+  - hamster
+  - zebrafish
+  - fish Nothobranchius guentheri
+
+Column: sex
+Enumerations:
+  - male
+  - female
+  - all
+  - hermaphrodites
+  - not specified
+  - None
+
+Column: effect_on_lifespan
+Enumerations:
+  - increases lifespan
+  - no change
+  - decreases lifespan
+  - increases lifespan in animals with decreased lifespans
+  - decreases survival under stress conditions
+  - improves survival under stress conditions
+  - decreases life span in animals with increased lifespans
+  - no change under stress conditions
+
+Column: diet
+Enumerations:
+  - standard chow
+  - None
+  - Purina  Lab  Diet  5001, ad libitum
+  - Purina Lab Diet 5001, from birth to 12 weeks ad. lib., then 40% from ad. lib.
+  - Teklad LM485 Diet, ad libitum
+  - Teklad 2018S Diet, ad libitum
+  - E. coli OP50, NGM
+  - 96W chow ad.lib.
+  - calorie-restricted diet
+  - 2% yeast, 10% sucrose, 5% cornmeal
+  - 2% yeasts, 10% sucrose, 5% cornmeal
+  - high-calorie food, 15% dextrose, 15% yeast, 2% agar
+  - low-calorie food, 5% dextrose, 5% yeast, 2% agar
+  - ad libitum
+  - agar, corn meal, yeast and molasses
+  - E. coli HT115 L4440, NGM
+  - E. coli HT115 L4440, optimal, 10^9, S basal medium
+  - E. coli HT115 L4440, restricted, 10^8, S basal medium
+  - E. coli HT115 L4440, ad libitum, 10^10, S basal medium
+  - Harlan Teklad, standart rodent chow, ad libitum
+  - cornmeal agar
+  - 18.2% protein, 4.8% fat, 6.6% mineral blend, 5.0% fiber ad. lib.
+  - 18.2% protein, 4.8% fat, 6.6% mineral blend, 5.0% fiber, 30% decreased ratio
+  - sugar-yeast medium
+  - agar, starvation
+  - Teklad Global Rodent  Diet, 5% fat,18%  protein,  57%  carbohydrate,  and  20%  other  components, ad libitum
+  - 9% fat and 20% protein Purina Picolab® Mouse 20, ad libitum
+  - agar, molasses, malt extract, Brewer's yeast, corn flour, soy flour, propionic acid, methyl-p-benzoate, Nipagin
+  - Purina Lab Chow 5010, ad libitum
+  - chow №1314, Altromin
+  - kanamycin-killed OP50-1 until day 2 of adulthood, then intermittent fasting
+  - kanamycin-killed OP50-1, ad libitum
+  - NIH-07 rodent chow ad.lib.
+  - OP50 E. coli, NGM from L1 to L4, then dsRNA expressing bacteria
+  - UV-killed E. coli OP50, NGM
+  - cornmeal, soy flour, yeast
+  - E. coli HT115 L4440, ad libitum, 10^10, NGM
+  - E. coli K12 L1-L4 sstages, E. coli HT115 L4440, days 0-5 of adult stage, then — anxenic media
+  - NGM, bacterial strain is not specified
+  - Harlan Teklad 2916, ad libitum
+  - 0,8% cornmeal, 10% sugar, 8% yeast
+  - CRM pelleted maintenance diet, Special Diet Services
+  - cornmeal-sugar-agar media and yeast paste
+  - 1.0 Sugar-yeast food medium
+  - S medium, bacterial strain is not specified
+  - CRM diet, Special Diet Services, UK, ad libitum
+  - PicoLab Rodent 20 5053, ad libitum
+  - cornmeal agar 1%
+  - sugar yeast diet
+  - sugar yeast diet 15%
+  - sugar-yeast diet with agar but no propionic acid
+  - sugar-yeast diet with agar and propionic acid
+  - sugar-yeast diet with corn
+  - cornmeal sucrose food
+  - cornmeal sucrose low calorie food
+  - cornmeal agar, starvation from day 10
+  - dead HT115 L4440 E. coli
+  - standart medium, 100 g/L brewer's yeast, 100 g/L sucrose, 20 g/L agar, and 10 mg/L tegosept
+  - diluted shugar-yeast medium, concentration 0.1N
+  - diluted shugar-yeast medium, concentration 0.5N
+  - diluted shugar-yeast medium, concentration 0.7N
+  - concetrated shugar-yeast mediun, concentration 1.5N
+  - diluted shugar-yeast medium, concentration 0.3N
+  - cornmeal agar, starvation from day 40
+  - cornmeal, yeast, sugar and agar, with methylparaben
+  - liquid S Medium
+  - 6% cornmeal, 3% yeast, 3% sugar, 6% glucose, 0.6% agar
+  - 0.45% agar, 5% dextrose, 2.5% sucrose, 8.3% cornmeal, 1.5% dried yeast, 0.06% phosphoric acid, and 0.4% propionic acid
+  - low-fat diet, 4% fat
+  - LabDiet product #5053, ad libitum
+  - Altromin pellet diet, ad libitum
+  - chow containing 17% protein, 11% fat and 3.5% fiber, ad libitum
+  - V1124-3, ssniff®, ad libitum
+  - 18% protein rodent diet, Harlan
+  - high fat diet
+  - high-carbohydrate/low-fat diet, 41.7% protein, 41.1% carbohydrate, 17.2 fat, ad libitum
+  - high-carbohydrate/high-fat diet, 16% protein, 41% carbohydrate, 43% fat, ad libitum
+  - low-carbohydrate/high-fat diet, 45% protein, 11.5% carbohydrate, 43.5% fat, ad libitum
+  - yeast medium
+  - regular rodent chow D12330
+  - 4RF21 GLP certificate, Mucedola srl; 12.0% water, 18.5% protein, 3.0% fat, 6.0% fiber, 7.0% ash; metabolizable energy, 2,668 kCal/kg
+  - rodent chow Glen Forrest Stockfeeders, no. AIN93G
+  - 124g sucrose, 31g yeast, 53g cornmeal, 8.9g agar and 2.6g Nipagin® M per litre
+  - 5% sucrose, 10% brewer's yeast, 1.5% agar, 0.3% Nipagin® M and 0.3% v/v propionic acid
+  - Purina  Lab  Diet  5001, 10% restriction from 6 to 8 weeks, then 25% restriction from 8 to 10 weeks and then 40% restriction from 10 weeks
+  - 5053 PicoLab Diet; Purina, St. Louis, MO
+  - LabDiet 5L79, ad libitum
+  - Harland-Tekald CRD TAM400
+  - RMH 3000 chow diet, Prolab, ad libitum
+  - корм RMH 3000, Prolab, ограниченная диета, 60% от ad libitum
+  - E. coli OP50 OD=3
+  - E.coli OP50 OD=1.50
+  - E.coli OP50 OD=0.50
+  - E.coli OP50 OD=0.25
+  - E.coli OP50 OD=0
+  - E. coli OP50, liquid medium
+  - E.coli HT115, liquid medium
+  - стерилизованный облучением корм для племенных животных стандарта JAX SHOOBREE® 84
+  - 0.7% agar, 1.0% soya flour, 8.0% polenta/maize, 1.8% yeast, 8.0% malt extract, 4.0% molasses, 0.8% propionic acid, and 2.3% nipagen
+  - cornmeal, molasses
+  - 0.65% agar, 10% glucose, 4% dry yeast, 5% corn flour and 3% rice
+  - 2.5% sugar, 2.5% yeast, 1.5% agar
+  - 150 g/L sucrose, 150 g/L autolyzed yeast, 20 g/L cornmeal, and 20 g/L agar
+  - E.coli OP50-1 (streptomycin resistant), NGM
+  - standart food, 8.6% cornmeal, 2.5% yeast, 5% dextrose, 2%	agar and 0.1 each of orthophosphoric and propionic acids
+  - sugar-yeast diet 6:1, yeast 2.8%;  sugar 17.2%; agar 2%; orthophosphoric acid 0.1%; propionic acid 0.1%
+  - sugar-yeast diet 1:1, yeast 10%; sugar 10%; agar 2%; orthophosphoric acid 0.1%; propionic acid 0.1%
+  - sugar-yeast diet 1:6, yeast 17.2%; sugar 2.8%; agar 2%; orthophosphoric acid 0.1%; propionic acid 0.1%
+  - UV-killed E. coli OP50, a 10-fold dilution, NGM
+  - LabDiet 5012, Purina Mills, St. Louis, MO
+  - Altromin GmbH
+  - 5% yeast, 10% sucrose, 5% cornmeal, 0.6% agar
+  - Teklad 22/5, 5% fat, 22% protein, 40% carbohydrate
+  - yeast agar glucose medium
+  - 2018 Teklad Global, Harlan Teklad, ad libitum
+  - PicoLab Rodent Diet 20
+  - 10% fat diet, Research Diet, ad libitum
+  - 60% fat diet, Research Diet, ad libitum
+  - soy based food Dyets, Inc., AIN-93M, Bethlehem, PA supplemented with 0.25 mg/g Neu5
+  - CE-2, Crea Japan Inc., ad libitum
+
+
+Column: intervention_deteriorates
+Note: This column contains comma-separated values of multiple biological processes/systems that deteriorate. Use LIKE queries with wildcards to search for specific processes. Refer to the biological processes list provided at the beginning of this prompt.
+
+Column: intervention_improves
+Note: This column contains comma-separated values of multiple biological processes/systems that improve. Use LIKE queries with wildcards to search for specific processes. Refer to the biological processes list provided at the beginning of this prompt.
+
+Column: main_effect_on_lifespan
+Enumerations:
+  - loss of function
+  - switch of function
+  - gain of function
+
+Column: intervention_way
+Enumerations:
+  - changes in genome level
+  - combined (inducible mutation)
+  - interventions by selective drug/RNAi
+
+Column: intervention_method
+Enumerations:
+  - gene knockout
+  - gene modification to affect product activity/stability
+  - gene modification
+  - additional copies of a gene in the genome
+  - addition to the genome of a dominant-negative gene variant that reduces the activity of an endogenous protein
+  - treatment with vector with additional gene copies
+  - gene modification to reduce protein activity/stability
+  - interfering RNA transgene
+  - RNA interferention
+  - gene modification to increase protein activity/stability
+  - introduction into the genome of a construct under the control of a gene promoter, which causes death or a decrease in the viability of cells expressing the gene
+  - knockout of gene isoform
+  - tissue-specific gene knockout
+  - reduced expression of one of the isoforms in transgenic animals
+  - gene modification to reduce gene expression
+  - treatment with gene product inducer
+  - None
+  - tissue-specific gene overexpression
+  - additional copies of a gene in transgenic animals
+  - treatment with a gene product inhibitor
+  - treatment with protein
+  - gene modification to increase gene expression 
+  - removal of cells expressing the gene
+  - splicing modification
+
+Column: tissue
+Enumerations:
+  - None
+  - muscle
+  - neurons
+  - fat body
+  - dopaminergic neurons
+  - glia
+  - brain
+  - corpora cardiaca
+  - insulin-producing cells
+  - central nervous system
+  - intestine
+  - liver
+  - heart
+  - myeloid cells
+  - intestinal stem cells and enteroblasts
+  - adipose tissue
+  - melanocytes,Trp2 expressing neurons
+  - cardiomyocytes
+  - hepatocytes
+  - heart,skeletal muscles
+  - heart,brain,skeletal muscles
+  - skin
+  - eye
+  - connective tissue
+  - cholinergic neurons
+  - kidney,brain
+  - kidney,heart,brain
+  - neurolemma
+  - hypodermis
+  - mediobasal hypothalamus
+  - motor neurons
+  - median neurosecretory cells
+  - hypocretin expressing neurons in the hypothalamus
+  - body wall muscles
+  - pharynx
+  - digestive tract
+  - abdominal fat and the digestive tract
+  - skeletal muscles
+  - white adipose tissue
+
+Column: tissue_specific_promoter
+Enumerations:
+  - None
+  - elav-GAL4
+  - elav-GeneSwitch-GAL4
+  - MHC-GeneSwitch-GAL4
+  -  S1-106-GAL4
+  - SH32-GAL4
+  - repo-GAL4
+  - c739-GAL4
+  - c309-GAL4
+  - Rulifson-GAL4
+  - Shen-GAL4
+  - Rulifson
+  - myo-3
+  - rab-3
+  - vha-6
+  - EEF1A1 (human)
+  - hsp70-HP1-eGFP
+  - a-MHC (rat)
+  - dilp2-GAL
+  - INS (C. elegans)
+  - INS (human)
+  - NES
+  - elav‐GAL4
+  - esg-GAL4, GAL80ts
+  - esg-GAL4; G80ts
+  - 5961-GeneSwitch-GAL4  (5961GS)
+  - actin-GAL4; Tubulin-Gal80TS (ActTS)
+  - FABP4 (mice)
+  - MHC-GAL4
+  - C/EBPβ (rat)
+  - Tub-GS
+  - S106-GS-GAL4
+  - act-GS
+  - S32-P{Switch}-GAL4
+  - S106-P{Switch}-GAL4
+  - S13-P{Switch}-GAL4
+  - MB221-P{Switch}-GAL4
+  - ELAV-GeneSwitch-GAL4
+  - elavGS-GAL4
+  - ubi-GAL4
+  - GMR-GAL4
+  - arm-GAL4
+  - FLP3
+  - D42-Gal4
+  - hsp70:FLP1; actin5C
+  - PRNP (mice)
+  - esg-GAL4 
+  - elav-GeneSwitch-GAL4 
+  - actin5C-GAL4
+  - elav-GAL4 
+  - cha-GAL4
+  - repo-GAL4 
+  - S1-106-GAL4
+  - S1-106-Gal4
+  - tubulin-GAL4
+  - elav-GeneSwitch
+  - armG4
+  - tinG4
+  - hsp70-GAL4
+  -  esg-GAL4, tub-GAL80ts
+  - 5961GS
+  - MHC-GAL4; Tub-GAL80/+ 
+  - C155-GAL4; Tub-GAL80/+
+  - Mef2-GAL4
+  - 24B-GAL4
+  - elavC155-GAL4
+  - DJ757-GAL4
+  - elav-GeneSwitch-Gal4
+  - hsp70 promoter
+  - pCAG
+  - da-GAL4
+  - D42-GAL4
+  - DJ634-GAL4
+  - CDKN2A
+  - mouse αMHCp (α-myosin heavy chain promoter)
+  - dilp2-GAL4
+  - HCRT (mice)
+  -  elav-GAL4
+  - OK107-GAL4
+  - C23-GAL4
+  - Arm-GAL4
+  - Appl-GAL4
+  - OK107-GAL4 
+  - Tub-GAL4
+  - human α-skeletal actin gene promoter
+  - TIGS-2-GAL4
+  - esg-GAL4
+  - S1106-GAL4
+  - MYL2 (rat)
+  - ACTA1 (human)
+  - 1407-GAL4
+  -  Elav-GS
+  - Act5C-GS
+  - the RNA polymerase II large subunit promoter
+  - CAG
+  - daGS>UAS
+  - dMef2-GAL4; GAL80ts
+  - da-GS-GAL4
+  - 7TetO
+  - D42-Gal4; 7TetO
+  - D42-; 7TetO
+  - UAS-da-Gal4
+  - UAS-da-GSG 
+  - cytomegalovirus promoter
+  - dpy-30p
+  - Tubulin-Gal4
+  - Tubulin-GeneSwitch
+  - Elav-GeneSwitch
+  - UAS (no GAL4)
+  - Tubulin-GAL4
+  - ppl-GAL4
+  - C16C10
+  - tinHE-Gal4
+
+Column: drug
+Enumerations:
+  - None
+  - tamoxifen
+  - mifepristone RU486
+  - AAV9-mTERT
+  - MCMV-TERT
+  - interfering RNA expressing bacteries
+  - auxin
+  - heat shock
+  - heat pulse
+  - Ex8[Pcdc-48.1::cdc-48.1]
+  - tetracycline
+  - EUK-008
+  - EUK-134
+  - interfering RNA expressing bacteries 1:1000
+  - interfering RNA expressing bacteries 1:50
+  - interfering RNA expressing bacteries 1:10
+  - DL-beta-hydroxybutyrate
+  - DL-beta-hydroxybutyrate + sodium butirate
+  - lentiviruses, expressing DN-IkB-a
+  - rapamycin
+  - AP20187
+  - quinic acid
+  - Cdc42 activity-specific inhibitor
+  - Rosizlitazone
+  - lentiviruses expressing constitutively active IKK-betta
+  - Ex008[SKN-1 S393A::GFP]
+  - captopril
+  - Recombinant mouse serum albumin rMSA
+  - doxycycline
+  - Ethanol
+  - interferring RNA
+  - MCMV-FST
+
+Column: treatment_start
+Enumerations:
+  - None
+  - 6weeks
+  - 0days
+  - 420days
+  - 720days
+  - 18months
+  - 0
+  - 3days
+  - 7days
+  - 10days
+  - 12days
+  - 14days
+  - 16days
+  - 18days
+  - 20days
+  - 2days
+  - 1days
+  - 8months
+  - 0months
+  - 5days
+  - 21days
+  - 17months
+  - 12months
+  - 35days
+  - 20months
+  - 525days
+  - 5months
+  - 14months
+  - 30days
+  - 26days
+  - 10weeks
+  - 9months
+  - 36weeks
+  - 22days
+  - 43days
+
+Column: treatment_end
+Enumerations:
+  - None
+  - 6.7weeks
+  - 5days
+  - 7days
+  - 14days
+  - 21days
+  - 6days
+  - 44days
+  - 23months
+  - 10days
+  - 529days
+  - 22days
+  - 43days
+
+
+
+### gene_criteria Table
+```sql
+CREATE TABLE "gene_criteria" (
+  "HGNC" TEXT, -- gene symbol
+  "criteria" TEXT -- aging-related criteria the gene meets
+)
+```
+
+**Aging Research Criteria (12 total):**
+1. Changes in gene activity extend the mammalian lifespan
+2. Changes in gene activity extend the non-mammalian lifespan  
+3. Changes in gene activity reduce the mammalian lifespan
+4. Changes in gene activity reduce the non-mammalian lifespan
+5. Age-related changes in humans
+6. Age-related changes in mammals
+7. Age-related changes in non-mammals
+8. Changes in gene activity protect against age-related impairment
+9. Changes in gene activity enhance age-related deterioration
+10. Association of gene variants or expression levels with longevity
+11. Association of the gene with accelerated aging in humans
+12. Gene product regulates other aging-related genes
+
+### gene_hallmarks Table
+```sql
+CREATE TABLE "gene_hallmarks" (
+  "HGNC" TEXT, -- gene symbol
+  "hallmarks of aging" TEXT -- comma-separated aging hallmarks (MULTI-VALUE FIELD)
+)
+```
+**Note:** Use LIKE queries with wildcards to search this multi-value field. Refer to the hallmarks list above.
+
+### longevity_associations Table
+```sql
+CREATE TABLE "longevity_associations" (
+  "HGNC" TEXT, -- gene symbol
+  "polymorphism type" TEXT, -- polymorphism type (SNP, VNTR, In/Del)
+  "polymorphism id" TEXT, -- polymorphism id (from dbSNP)
+  "nucleotide substitution" TEXT, -- nucleotide substitution
+  "amino acid substitution" TEXT, -- amino acid substitution
+  "polymorphism — other" TEXT, -- other common names for polymorphism
+  "ethnicity" TEXT, -- ethnicity of participants in studied cohorts
+  "study type" TEXT, -- design of population study (GWAS, candidate genes study, meta-analysis, etc.)
+  "sex" TEXT, -- sex of participants in studied cohorts
+  "doi" TEXT, -- doi of the article
+  "pmid" REAL -- pmid of the article
+)
+```
+
+### gene_criteria Table Enumerations
+
+**Column: criteria**
+- 'Age-related changes in gene expression, methylation or protein activity'
+- 'Age-related changes in gene expression, methylation or protein activity in humans'  
+- 'Association of genetic variants and gene expression levels with longevity'
+- 'Regulation of genes associated with aging'
+- 'Changes in gene activity extend non-mammalian lifespan'
+- 'Changes in gene activity protect against age-related impairment'
+- 'Age-related changes in gene expression, methylation or protein activity in non-mammals'
+- 'Changes in gene activity extend mammalian lifespan'
+- 'Changes in gene activity reduce mammalian lifespan'
+- 'Changes in gene activity enhance age-related deterioration'
+- 'Changes in gene activity reduce non-mammalian lifespan'
+- 'Association of the gene with accelerated aging in humans'
+
+### longevity_associations Table Enumerations
+Column: polymorphism type
+Enumerations:
+  - SNP
+  - In/Del
+  - n/a
+  - haplotype
+  - VNTR
+  - PCR-RFLP
+
+Column: amino acid substitution
+Enumerations:
+  - n/a
+  - T/M
+  - V/M
+  - S/G
+  - Ile229Val
+  - Ser31Arg
+  - I405V
+  - Lys751Gln
+  - Asn/Ser
+  - Phe352Val
+  - K153R
+  - Thr/Ala
+  - Thr/Ile
+  - Gly/Gly
+  - Q192R
+  - Pro12Ala
+  - Ala/Val
+  - Arg72Pro
+  - T119M
+  - Leu1074Phe
+
+Column: polymorphism — other
+Enumerations:
+  - n/a
+  - E2, E3, E4
+  - E4
+  - E2
+  - APOE[rs449647+rs769446+rs405509+rs429358+rs7412]+HRAS[rs8176330+rs8176331+rs8176332+rs8176333+rs8176334+rs8176335+rs12628]+LASS1[rs60774903+rs3746263+Exon1-234
+  - TaqIB
+  - 3'UTR VNTR
+  - PvuII
+  - 680
+  - d3-GHR
+  - HLA-DR
+  - IGF1R[G/A]+IRS2[Gly/Asp],+UCP2[Ala/Val]
+  - ApaI
+  - TH[STR]+IGF2[AvaII]
+  - TH[STR]+INS[FokI]
+  - Alu element insertion/deletion
+  - MNS16A
+  - rs1800592+C-3740A
+
+Column: ethnicity
+Enumerations:
+  - Caucasian, American
+  - European
+  - Greek
+  - Ashkenazi Jewish
+  - Polish
+  - Chinese
+  - Caucasian
+  - Italian
+  - Japanese
+  - Danish
+  - Spanish
+  - German
+  - European, East Asian, African American
+  - n/a
+  - Chinese, Han
+  - Italian, Southern
+  - German, American
+  - Caucasian, African-American
+  - East Asian, Europeans, Caucasian American
+  - Japanese American
+  - Italian, Calabrian
+  - Korean
+  - Belarusian
+  - mixed
+  - Caucasian, Ashkenazi Jewish
+  - Dutch
+  - Amish
+  - French
+  - Ashkenazi Jewish, Amish, Caucasian
+  - Japanese, Okinawan
+  - North-eastern Italian
+  - Tatars
+  - American, Caucasians; Italian, Southern; French; Ashkenazi Jewish
+  - Chinese, Bama Yao, Guangxi Province
+  - Swiss
+  - German, Danes, French
+  - American, Caucasian
+  - Italian, Central
+  - Finnish
+
+Column: study type
+Enumerations:
+  - GWAS
+  - iGWAS
+  - candidate genes study
+  - gene-based association approach
+  - family study
+  - single-variant association approach
+  - meta-analysis of GWAS, replication of previous findings
+  - meta-analysis of GWAS
+  - GWAS, discovery + replication
+  - GWAS, replication
+  - meta-analysis of GWAS, replication
+  - n/a
+  - meta-analysis of candidate gene studies
+  - immunochip, discovery + replication
+  - immunochip
+
+Column: sex
+Enumerations:
+  - all
+  - male
+  - not specified
+  - female
+
+---
+
+## Example Query Patterns
+
+### Common Query Types
+
+**1. Find genes with specific effects (ordered by magnitude):**
+```sql
+-- Genes that increase lifespan, ordered by greatest extension first
+SELECT HGNC, model_organism, effect_on_lifespan, lifespan_percent_change_mean 
+FROM lifespan_change 
+WHERE effect_on_lifespan = 'increases lifespan'
+ORDER BY lifespan_percent_change_mean DESC;
+
+-- Genes that decrease lifespan, ordered by greatest reduction first
+SELECT HGNC, model_organism, effect_on_lifespan, lifespan_percent_change_mean 
+FROM lifespan_change 
+WHERE effect_on_lifespan = 'decreases lifespan'
+ORDER BY lifespan_percent_change_mean ASC;
+
+-- Genes associated with specific hallmarks
+SELECT gh.HGNC, gh."hallmarks of aging"
+FROM gene_hallmarks gh
+WHERE gh."hallmarks of aging" LIKE '%stem cell exhaustion%';
+```
+
+**2. Cross-table analysis:**
+```sql
+-- Genes with both lifespan effects and population associations
+SELECT DISTINCT lc.HGNC, lc.effect_on_lifespan, la.ethnicity
+FROM lifespan_change lc
+JOIN longevity_associations la ON lc.HGNC = la.HGNC
+WHERE lc.effect_on_lifespan = 'increases lifespan';
+```
+
+**3. Intervention effects:**
+```sql
+-- Genes that improve cardiovascular function
+SELECT HGNC, intervention_improves, effect_on_lifespan
+FROM lifespan_change 
+WHERE intervention_improves LIKE '%cardiovascular system%';
+```
+
+**4. Organism-specific queries:**
+```sql
+-- Mouse studies on specific genes
+SELECT * FROM lifespan_change 
+WHERE model_organism = 'mouse' AND HGNC = 'FOXO3';
+```
+
+Remember: Always use LIKE with wildcards (%) for multi-value fields (hallmarks, intervention effects).