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November 20, 2025 15:36
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Curated Google Drive Documents for METPO/KG-Microbe/CMM Work
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| Title | URL | Type | Notes | |
|---|---|---|---|---|
| 2022-10-24: BER update | https://docs.google.com/presentation/d/1Q6FV8VGCxTsVkGeUfaR-1c8CoWIRUNxpizAq2QdIbkU | Google Slides | BER project update (Oct 2022) | |
| 2025_DOE_BER_CM_REE | https://drive.google.com/drive/folders/1WAmbFZuMw8-Oq6GxTe63XxJP1wmihmrM | Folder | 2025 DOE BER Critical Minerals & REE project folder | |
| Agenda Kickoff Meeting for FY25 CMM Projects.pdf | https://drive.google.com/file/d/1K_HHrQC2DlsYEb2MTh67carptXVGE3ZL | FY25 CMM kickoff meeting agenda | ||
| BER CMM 2025 AI | https://docs.google.com/document/d/1Zd_zSUCzY9nBbgR0Q-co8otFSid0RB57Glnk8sHUwSc | Google Doc | BER Critical Minerals & Materials AI project document (2025) | |
| BER CMM AI Project Map | https://docs.google.com/spreadsheets/d/1y36vxDcfs6ZxqelfpxJMC5Nw91Q5aqGVZedZ3kpGEnA | Google Sheet | Project mapping/organization for CMM AI work | |
| BER CMM AI Task 1.1 | https://docs.google.com/presentation/d/1nwbHXUDZXv1YxPM2a5SJomLmIv-huEHcFKNzZr8o9mg | Google Slides | Task 1.1 presentation for BER CMM AI | |
| BER CMM Data for AI - for editing | https://docs.google.com/spreadsheets/d/1h-kOdyvVb1EJPqgTiklTN9Z8br_8bP8KGmxA19clo7Q | Google Sheet | Active data compilation for CMM AI (editable version) | |
| BER CMM Data for AI OBSOLETE | https://docs.google.com/spreadsheets/d/1vUofqjZFBkYO-MM01BnE65ErMgTHhEX7ef6dVBCCv0I | Google Sheet | Superseded version of CMM AI data | |
| BER_Data_Transfer_Meeting_20231204 | https://docs.google.com/document/d/1F76pAZP3N5qdspgDqLDDqPXVBzSnSgoacM-5uCK8NO4 | Google Doc | BER data transfer meeting notes (December 2023) | |
| Biolog OntoGPT schema | https://docs.google.com/document/d/12StdeehVcpPOQq9HvHskH1OIovcgKQnxr3VtZkl06rs | Google Doc | OntoGPT schema design for Biolog data extraction | |
| Biolog OntoGPT simple | https://docs.google.com/document/d/17P1AaEFcXLKQZp844C9VpzRx5U0VXnSfvdjkCQFZR2U | Google Doc | Simplified Biolog phenotype extraction with OntoGPT | |
| Biome features: semantically labeled abundances and friends | https://docs.google.com/presentation/d/1bkasa14pEQ5jby2zgV7y68wskco2bTnPzaAmqhcMrIs | Google Slides | Presentation on biome feature semantic labeling | |
| CMM_genomes | https://drive.google.com/drive/folders/1HadLkfQ6mRJzqf3kISsIvPD4UXKJDrEY | Folder | Folder containing CMM-related genome data | |
| cmm_pdfs | https://drive.google.com/drive/folders/1xY4hvPfehP1mfZhTp9uuLo6mlQSMp6y0 | Folder | Folder with CMM-related PDF documents | |
| CMM-REE chassis engineering | https://docs.google.com/presentation/d/1shMZFm8YuPNOke0xsrGbs3dDW59uvWoRSaexN41Zqi8 | Google Slides | Presentation on chassis engineering for CMM/REE | |
| DSM: CultureBot and KG-Microbe - Modular and Scalable Knowledge Graphs 20250519 | https://docs.google.com/presentation/d/1mFqkGMyO6NwwGfkaDhRaPfd-M7Q6c_6GJKTCtA4Fc6M | Google Slides | DSM presentation on CultureBot and KG-Microbe (May 2025) | |
| EGSB Accomplishments FY24-FY26 | https://docs.google.com/document/d/1ru_DrM2qP-QzWXSIZ0dS_yYTs6yY5gLT6MNY2p-pd9I | Google Doc | Current Environmental Genomics and Systems Biology accomplishments | |
| EGSB Research Group December Update | https://docs.google.com/presentation/d/1b2GkIpN0nr8hs2gCg5zwwC31AIp3QHlg7UMgWjpfUrY | Google Slides | December research group update | |
| From the OBO Foundry to the Molecular Foundry: Semantic data integration and ontologies for ML and AI | https://docs.google.com/presentation/d/1BBi2bnkX7YF-Q-PPOWQIjG9WkiUWlxUGTeyUPfGtKRI | Google Slides | Presentation bridging OBO Foundry and Molecular Foundry | |
| FY21 COVID-19 LDRD 2020-08-21 | https://docs.google.com/presentation/d/18K_xlmMLUBtyJIOVCi1pw2wXi9hIAmAX01Rqm3A816w | Google Slides | FY21 COVID-19 LDRD proposal | |
| icbo_metpo_slides.pdf | https://drive.google.com/file/d/1hzyjXk-ZrPM1Hsx3GFCbgDbgUZuLr4bT | ICBO conference slides for METPO | ||
| Joachimiak biosketch - DOE BER 2025 | https://docs.google.com/document/d/1ETTYIvCf3QqnlxlyOqPzmUnqEpv6DULloTH9Y0PFnqs | Google Doc | Biosketch for DOE BER 2025 proposals | |
| KG-Microbe and CultureBot - KBase 20240201 | https://docs.google.com/presentation/d/1nC2OngFtUCzyw4G5NaN60ZIPhtFZAgrY5Sv848uVlHU | Google Slides | KBase presentation (Feb 2024) | |
| KG-Microbe Data Products (NERSC, S3, GitHub) | https://docs.google.com/document/d/1jJm2nd4FUv6bdOPGa7MPAg5GXudwvt0TAHiniK1ZYF0 | Google Doc | Documentation of KG-Microbe data locations, releases, and downloads | |
| kg-microbe folder | https://drive.google.com/drive/folders/1kNUNd0J8GhoPkFDitsujtuiHPUWkv7bG | Folder | Main folder for KG-Microbe files | |
| KG-Microbe manuscript work punch list | https://docs.google.com/document/d/1o-fLUa4vj92uDOE6rMNDkjOAeK4jqPVXOFrGfeE1GzA | Google Doc | Task list for paper submission; includes before/after submission tasks, release procedures, provenance tracking, asset creation workflow | |
| KG-Microbe paper | https://docs.google.com/document/d/1v9ay8B80aVf6lQTEYvQoJY56YsxGy21VTHFa2PBFZUE | Google Doc | Main manuscript draft | |
| Knowledge Graph Approaches vs. Bayesian Optimization for Microbial Media Discovery CLAUDE | https://docs.google.com/document/d/1kHF0LO_LTPJlEfXY3vntSC_eYD_1oCeVpZTqNMHC0jk | Google Doc | Comparison/analysis document for media discovery approaches | |
| Lanthanide metabolism example | https://docs.google.com/document/d/1z0UoOkzqruy8cIFICHdRaQJcw4x0PtEwC7dBRViYB-g | Google Doc | Example/case study of lanthanide metabolism representation in METPO/KG-Microbe | |
| LBL/BacDive/DSMZ 2025-07-02 | https://docs.google.com/document/d/1B9CMKy9DSL_euUqBeUcan4prbYeC0765g4z0b-kG1q0 | Google Doc | Meeting notes from July 2025 with BacDive/DSMZ collaboration | |
| LDRD 2024 Notes | https://docs.google.com/document/d/10JDfDCVw8g7V1IjU28Bo8qLt9hFpYvfmS2_1HlK-uMA | Google Doc | CultureBot LDRD proposal notes; includes Deutschbauer feedback, Susannah suggestions, host-association inference strategy, FY2023 oral feedback | |
| LDRD running meeting notes | https://docs.google.com/document/d/13D72S6EoI1S5zHYiOJYpMjqar7hwSTU8uR4_SvNjNbI | Google Doc | Ongoing meeting notes for LDRD proposals and discussions | |
| Lorenz/Julia request for integrated, up-to-date BacDive schema and data | https://docs.google.com/document/d/1eKPeIT_UxTq0dvgULb9dr-ack0xH47uyCKaNoMChits | Google Doc | Request documentation for BacDive integration needs | |
| Mark-METPO-2025-11-11-v2.pdf | https://drive.google.com/file/d/1M_8H28t4vSqHRk2SZNJU3YubJIvQx--5 | Updated version of METPO presentation (duplicate 1) | ||
| Mark-METPO-2025-11-11-v2.pdf | https://drive.google.com/file/d/1fwmWUUcu4D9hK6w17KO04R_Kgt4tD64F | Updated version of METPO presentation (duplicate 2) | ||
| Mark-METPO-2025-11-11-v2.pdf | https://drive.google.com/file/d/1t9g8lP4SaGTXnkh6dQjSNr4HiU2ndmrw | Updated version of METPO presentation (duplicate 3) | ||
| Mark-METPO-2025-11-11.pdf | https://drive.google.com/file/d/140vtQlbky2BjESkITUXK3Kwwfav1ETsT | METPO presentation/slides from Nov 2025 | ||
| METPO ancient history | https://docs.google.com/spreadsheets/d/1Oc-nfEkwkwIKdT2wMQNzK4iDiDWhC55ZIhsuJPZhves | Google Sheet | Historical development notes/data for METPO | |
| METPO Short Talk Abstract for ICBO 2025 | https://docs.google.com/document/d/1HoN6yE-NBsjNms5DmEShNS4QCi5oqHLWyGwmQ2_yfQ0 | Google Doc | Draft abstract for ICBO 2025; includes evidence-based arguments, ontology coverage analysis, fragmentation statistics, OBO Foundry principles discussion | |
| metpo_sheet.tsv | https://docs.google.com/spreadsheets/d/19T2jBfEuL19EkZijPSgYNrj5WBN1pcFD | Google Sheet | Main METPO term template/sheet | |
| metpo-qualified-exact--synonyms.tsv | https://docs.google.com/spreadsheets/d/1J6Yreg6_kMCHQUnDQon7iyUvJt6nR5oG | Google Sheet | Exact synonyms for METPO terms | |
| metpo-qualified-related-synonyms.tsv | https://docs.google.com/spreadsheets/d/1F1zJBgW3U7nzJHWPiXQF1re0wiE31jDa | Google Sheet | Related synonyms for METPO terms | |
| micro ontology oddities | https://docs.google.com/document/d/1Zce_Lf3neNcOvwFd8ZOJCoz6xZ5aC1KgDftuLK7Hjy0 | Google Doc | Documentation of issues and oddities found in the MicrO ontology | |
| Microbial trait databases (BacDive, BactoTraits, etc.) are most useful when semantically normalized | https://docs.google.com/document/d/1sGEQ1BYNueyfDWJxqJ-u18w3xGw-lOvT5n8lwaUhxOg | Google Doc | Unlabeled document (needs investigation) | |
| Mining with Microbes: America's AI-Driven Critical Materials Solution | https://docs.google.com/document/d/1AfmxUP8L_5TFGZcReQpzBmRGZkHGISaepAVaZ3qBHd0 | Google Doc | Project summary/proposal for microbial critical minerals recovery | |
| Mungall_FY23_EGSB_JGI LDRD - Division | https://docs.google.com/presentation/d/1BgZGKzb-t5bMNBnsrnR9Ue63NzdLvTbaCAGwAelGPhY | Google Slides | Mungall LDRD presentation FY23 | |
| Oct 16, 2025 Critical minerals | https://docs.google.com/document/d/1aRxeH5ljcMSM3W3ozHecn46NlZlfnTyuE5cN9mSzoxI | Google Doc | Recent critical minerals meeting notes | |
| Old EGSB Accomplishments (before Oct 2023) | https://docs.google.com/document/d/1XMKdw3h-inAL359azVyBw5mDadFBmH9yZqqYHfu4U80 | Google Doc | Historical EGSB accomplishments archive | |
| OntoGPT | https://drive.google.com/drive/folders/1PZrzFiyEQklbHJFMv793-Uc6EIdS7rkw | Folder | Main OntoGPT folder | |
| OntoGPT Conclave Notes | https://docs.google.com/document/d/1oOTZvyKFQfEuY1GHsI9DJ4sl-ZLe1FPrCicGQsrX6A8 | Google Doc | Meeting notes from OntoGPT conclave/workshop | |
| rare eath minerals in bbop slack | https://docs.google.com/document/d/1JpNrhMLLxS9rd5pYlpM98KJFKOA-TlVwG_eu4nOwRho | Google Doc | Slack conversation notes on REE/rare earth minerals | |
| Schema for the BacDive endpoint | https://docs.google.com/document/d/19DCab9950V34b1-gEbJagcAKb3pN86xaIbD0NRjTbOE | Google Doc | Documentation of BacDive API schema | |
| source ontologies for METPO? | https://docs.google.com/spreadsheets/d/1brHx27MGUk42G9VCbyY5vUX1F3Mb5Dr8gLM-e-SHj1s | Google Sheet | Unlabeled spreadsheet (needs investigation) | |
| Tools for Working with Biological Knowledge Graphs - Mar 9, 2021 | https://docs.google.com/presentation/d/1-xKJnH0q9FKOIZC_GOXZuLWAd3of3Ah-PeWFGtCQGLs | Google Slides | Tutorial/workshop on KG tools | |
| unified culturebot mapping proposal | https://docs.google.com/spreadsheets/d/1V9rjZSZgYHf4HsCwJBUnsVX7Gmn2AYszDQzI6b6ZhxA | Google Sheet | Mapping proposal for CultureBot term standardization | |
| https://drive.google.com/drive/folders/1A9oShPpWdUfkBvQ2goxhyIRf5xF-xSYQ |
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