Abstract
Hippocampome.org is a mature open-access knowledge base of the rodent hippocampal formation focusing on neuron types and their properties. Hippocampome.org v1.0 established a foundational classification system identifying 122 hippocampal neuron types based on their axonal and dendritic morphologies, main neurotransmitter, membrane biophysics, and molecular expression. Releases v1.1 through v1.12 furthered the aggregation of literature-mined data, including among others neuron counts, spiking patterns, synaptic physiology, in vivo firing phases, and connection probabilities. Those additional properties increased the online information content of this public resource over 100-fold, enabling numerous independent discoveries by the scientific community. Hippocampome.org v2.0, introduced here, besides incorporating over 50 new neuron types, now recenters its focus on extending the functionality to build real-scale, biologically detailed, data-driven computational simulations. In all cases, the freely downloadable model parameters are directly linked to the specific peer-reviewed empirical evidence from which they were derived. Possible research applications include quantitative, multiscale analyses of circuit connectivity and spiking neural network simulations of activity dynamics. These advances can help generate precise, experimentally testable hypotheses and shed light on the neural mechanisms underlying associative memory and spatial navigation.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
Minor editing changes.
Glossary of abbreviations
- 5HT-3
- serotonin receptor 3
- AA
- EC LII Axo-axonic cell
- AAC
- Axo-axonic cell
- ABA
- Allen Brain Atlas
- APampl
- action potential amplitude
- APwidth
- action potential width
- ASP.
- adapting spiking
- Astn2
- astrotactin 2
- BC
- Basket cell
- BC MP
- EC LII Basket-Multipolar cell
- BiC
- Bistratified cell
- BICCN
- BRAIN Initiative Cell Census Network
- C
- Capacitance
- CB
- calbindin
- CB1
- cannabinoid receptor type 1
- CCK+
- cholecystokinin-positive
- CR
- calretinin
- CSV
- comma-separated value
- Dcn
- decorin
- DG
- dentate gyrus
- E-E
- excitatory to excitatory
- E-I
- excitatory to inhibitory
- EC
- entorhinal cortex
- ENK
- enkephalin
- fAHP
- fast after-hyperpolarizing potential
- g
- conductance constant
- GABAa α1
- GABA-a alpha 1 subunit
- GC
- granule cell
- Gpc3
- glypican 3
- GPUs
- graphical processing units
- GRALDEN
- GRAnule-Like DENdrites
- Garci
- grid cell
- Grp
- gastrin releasing peptide
- GUI
- graphical user interface
- H
- hilus
- HIPROM
- Hilar Interneuron with PRojections to the Outer Molecular layer
- Htr2c
- 5-hydroxytryptamine receptor 2c
- I-E
- inhibitory to excitatory
- I-I
- inhibitory to inhibitory
- IS
- interneuron specific
- LI-II
- layers 1-2
- LII
- layer 2
- LIII
- layer 3
- Max FR
- maximum firing rate
- MEC
- medial entorhinal cortex
- MFA
- Mossy Fiber-Associated
- mGluR1a
- metabotropic glutamate receptor 1 alpha
- MOCAP
- cell with MOlecular Commissural-Associational Pathway-related axons and dendrites
- MOLAX
- MOlecular Layer Axons
- MP PC
- EC LI-II Multipolar Pyramidal cell
- Mus2R
- muscarinic type 2 receptor
- NASP
- non-adapting spiking
- Ndst4
- N-deacetylase and N-sulfotransferase 4
- nNOS
- neuronal nitric oxide synthase
- Nov
- nephroblastoma overexpressed
- NPY
- neuropeptide Y
- Nr3c2
- nuclear receptor subfamily 3 group C member 2
- Nr4a1
- nuclear receptor subfamily 4 group A member 1
- ORAX
- ORiens AXons
- ORDEN
- ORiens DENdrites
- PC
- pyramidal cell / CA1 Pyramidal cell (Fig. 9B)
- PL
- polymorphic layer
- PoE
- pieces of evidence
- PoK
- pieces of knowledge
- Prss12
- serine protease 12
- Prss23
- serine protease 23
- PV+
- parvalbumin-positive
- QuadD-LM
- quadrilaminar dendrites – lacunosum-moleculare
- Rin
- input resistance
- RLN
- reelin
- sAHP
- slow after-hyperpolarizing potential
- SC
- MEC LII Stellate cell
- SD
- standard deviation
- SG
- stratum granulosum
- SL
- stratum lucidum
- SLM
- stratum lacunosum-moleculare
- SMi
- inner stratum moleculare
- SMo
- outer stratum moleculare
- SO
- stratum oriens
- SOM
- somatostatin
- SP
- stratum pyramidale
- SR
- stratum radiatum
- Sub
- subiculum
- SWR
- sharp-wave ripple
- SynGO
- synaptic gene ontologies
- T
- Temperature
- τd
- synaptic decay constant
- τf
- facilitation time constant
- τm
- membrane time constant
- τr
- recovery time constant
- TPM
- Tsodyks-Pawelzik-Markram
- TSTUT.
- transient stuttering
- TSTUT.PSTUT
- transient stuttering followed by persistent stuttering
- TSTUT.SLN
- silence preceded by transient stuttering
- U
- utilization ratio
- vGluT3
- vesicular glutamate transporter 3
- Vh
- holding potential
- VIP
- vasoactive intestinal polypeptide
- Vmin
- post-spike reset potential
- Vpeak
- spike cutoff potential
- Vr / Vrest
- resting membrane potential
- Vt / Vthresh
- firing threshold potential
- WA BC
- Wide-arbor Basket cell
- Wfs1
- wolframin ER transmembrane glycoprotein
