diff --git a/mkdocs.yml b/mkdocs.yml
index 484b08bb54..d2b665906d 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -48,6 +48,7 @@ nav:
         - MEG file formats: 99-appendices/06-meg-file-formats.md
         - MEG systems: 99-appendices/07-meg-systems.md
         - Coordinate systems: 99-appendices/08-coordinate-systems.md
+        - Entities: 99-appendices/09-entities.md
       - Changelog: CHANGES.md
     - The BIDS Starter Kit:
       - GitHub repository: https://github.com/bids-standard/bids-starter-kit
diff --git a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
index d7f047c2c7..054a78acc7 100644
--- a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
+++ b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
@@ -141,21 +141,20 @@ modalities include:
 If the structural images included in the dataset were defaced (to protect
 identity of participants) one MAY provide the binary mask that was used to
 remove facial features in the form of `_defacemask` files.
-In such cases,  the OPTIONAL `mod-<label>` key/value pair corresponds to modality suffix,
+In such cases,  the OPTIONAL [`mod-<label>`](../99-appendices/09-entities.md#mod)
+key/value pair corresponds to modality suffix,
 such as T1w or inplaneT1, referenced by the defacemask image.
 For example, `sub-01_mod-T1w_defacemask.nii.gz`.
 
-#### The `run` entity
-
-If several scans of the same modality are acquired they MUST be indexed with a
-key-value pair: `_run-1`, `_run-2`, `_run-3` etc. (only nonnegative integers are allowed as
+If several scans of the same modality are acquired they MUST be indexed with the
+[`run-<index>`](../99-appendices/09-entities.md#run) key-value pair:
+`_run-1`, `_run-2`, `_run-3` etc. (only nonnegative integers are allowed as
 run labels). When there is only one scan of a given type the run key MAY be
 omitted. Please note that diffusion imaging data is stored elsewhere (see
 below).
 
-#### The `acq` entity
-
-The OPTIONAL `acq-<label>` key/value pair corresponds to a custom label the user
+The OPTIONAL [`acq-<label>`](../99-appendices/09-entities.md#acq)
+key/value pair corresponds to a custom label the user
 MAY use to distinguish a different set of parameters used for acquiring the same
 modality. For example this should be used when a study includes two T1w images -
 one full brain low resolution and and one restricted field of view but high
@@ -168,9 +167,8 @@ can also be used to make that distinction. At what level of detail to make the
 distinction (e.g. just between RARE and FLASH, or between RARE, FLASH, and
 FLASHsubsampled) remains at the discretion of the researcher.
 
-#### The `ce` entity
-
-Similarly the OPTIONAL `ce-<label>` key/value can be used to distinguish
+Similarly the OPTIONAL [`ce-<label>`](../99-appendices/09-entities.md#ce)
+key/value can be used to distinguish
 sequences using different contrast enhanced images. The label is the name of the
 contrast agent. The key `ContrastBolusIngredient` MAY be also be added in the
 JSON file, with the same label.
@@ -184,9 +182,8 @@ fields specific to anatomical scans:
 | -----------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------- |
 | ContrastBolusIngredient | OPTIONAL. Active ingredient of agent. Values MUST be one of: IODINE, GADOLINIUM, CARBON DIOXIDE, BARIUM, XENON Corresponds to DICOM Tag 0018,1048. |
 
-#### The `rec` entity
-
-Similarly, the OPTIONAL `rec-<label>` key/value can be used to distinguish
+Similarly, the OPTIONAL [`rec-<label>`](../99-appendices/09-entities.md#rec)
+key/value can be used to distinguish
 different reconstruction algorithms (for example ones using motion correction).
 
 ### Task (including resting state) imaging data
@@ -217,16 +214,19 @@ multiband acquisitions, one MAY also save the single-band reference image as
 type `sbref` (e.g. `sub-control01_task-nback_sbref.nii.gz`).
 
 Each task has a unique label that MUST only consist of letters and/or numbers
-(other characters, including spaces and underscores, are not allowed).
+(other characters, including spaces and underscores, are not allowed) with the
+[`task-<label>`](../99-appendices/09-entities.md#task) key/value pair.
 Those labels MUST be consistent across subjects and sessions.
 
-If more than one run of the same task has been acquired a key/value pair:
-`_run-1`, `_run-2`, `_run-3` etc. MUST be used. If only one run was acquired the
+If more than one run of the same task has been acquired the
+[`run-<index>`](../99-appendices/09-entities.md#run) key/value pair MUST be used:
+`_run-1`, `_run-2`, `_run-3` etc. If only one run was acquired the
 `run-<index>` can be omitted. In the context of functional imaging a run is
 defined as the same task, but in some cases it can mean different set of stimuli
 (for example randomized order) and participant responses.
 
-The OPTIONAL `acq-<label>` key/value pair corresponds to a custom label one may
+The OPTIONAL [`acq-<label>`](../99-appendices/09-entities.md#acq)
+key/value pair corresponds to a custom label one may
 use to distinguish different set of parameters used for acquiring the same task.
 For example this should be used when a study includes two resting state images -
 one single band and one multiband. In such case two files could have the
@@ -235,22 +235,25 @@ following names: `sub-01_task-rest_acq-singleband_bold.nii.gz` and
 other label than `singleband` and `multiband` as long as they are consistent
 across subjects and sessions and consist only of the legal label characters.
 
-Similarly the OPTIONAL `ce-<label>` key/value can be used to distinguish
+Similarly the OPTIONAL [`ce-<label>`](../99-appendices/09-entities.md#ce)
+key/value can be used to distinguish
 sequences using different contrast enhanced images. The label is the name of the
 contrast agent. The key ContrastBolusIngredient MAY be also be added in the JSON
 file, with the same label.
 
-Similarly the OPTIONAL `rec-<label>` key/value can be used to distinguish
+Similarly the OPTIONAL [`rec-<label>`](../99-appendices/09-entities.md#rec)
+key/value can be used to distinguish
 different reconstruction algorithms (for example ones using motion correction).
 
-Similarly the OPTIONAL `dir-<label>` and `rec-<label>` key/values
+Similarly the OPTIONAL [`dir-<label>`](../99-appendices/09-entities.md#dir)
+and [`rec-<label>`](../99-appendices/09-entities.md#rec) key/values
 can be used to distinguish different phase-encoding directions and
 reconstruction algorithms (for example ones using motion correction).
 See [`fmap` Case 4](01-magnetic-resonance-imaging-data.md#case-4-multiple-phase-encoded-directions-pepolar)
 for more information on `dir` field specification.
 
-Multi-echo data MUST be split into one file per echo. Each file shares the same
-name with the exception of the `_echo-<index>` key/value. For example:
+Multi-echo data MUST be split into one file per echo using the
+[`echo-<index>`](../99-appendices/09-entities.md#echo) key-value pair. For example:
 
 ```Text
 sub-01/
@@ -374,7 +377,8 @@ sub-<label>/[ses-<label>/]
 ```
 
 Diffusion-weighted imaging data acquired for that participant. The OPTIONAL
-`acq-<label>` key/value pair corresponds to a custom label the user may use to
+[`acq-<label>`](../99-appendices/09-entities.md#acq)
+key/value pair corresponds to a custom label the user may use to
 distinguish different set of parameters. For example this should be used when a
 study includes two diffusion images - one single band and one multiband. In such
 case two files could have the following names:
@@ -458,8 +462,10 @@ slashes. Here’s an example with multiple target scans:
 The IntendedFor field is OPTIONAL and in case the fieldmaps do not correspond to
 any particular scans it does not have to be filled.
 
-Multiple fieldmaps can be stored. In such case the `_run-1`, `_run-2` should be
-used. The OPTIONAL `acq-<label>` key/value pair corresponds to a custom label
+Multiple fieldmaps can be stored.
+In such case the [`run-<index>`](../99-appendices/09-entities.md#run) key/value pair should be
+used. The OPTIONAL [`acq-<label>`](../99-appendices/09-entities.md#acq)
+key/value pair corresponds to a custom label
 the user may use to distinguish different set of parameters.
 
 #### Case 1: Phase difference image and at least one magnitude image
@@ -581,7 +587,8 @@ example
 }
 ```
 
-`label` value of `_dir-` can be set to arbitrary alphanumeric label (`[a-zA-Z0-9]+` for
+The `label` value of the [`dir-<label>`](../99-appendices/09-entities.md#dir) key/value pair
+can be set to arbitrary alphanumeric label (`[a-zA-Z0-9]+` for
 example `LR` or `AP`) that can help users to distinguish between different
 files, but should not be used to infer any scanning parameters (such as phase
 encoding directions) of the corresponding sequence. Please rely only on the JSON
diff --git a/src/04-modality-specific-files/02-magnetoencephalography.md b/src/04-modality-specific-files/02-magnetoencephalography.md
index 4db21e503b..18ca0f529b 100644
--- a/src/04-modality-specific-files/02-magnetoencephalography.md
+++ b/src/04-modality-specific-files/02-magnetoencephalography.md
@@ -49,13 +49,13 @@ files of various nature: for example, CTF's `.ds` format, or BTi/4D.
 Yet other manufacturers split their files once they exceed a certain size
 limit. For example Neuromag/Elekta/Megin, which can produce several files
 for a single recording. Both `some_file.fif` and `some_file-1.fif` would
-belong to a single recording. In BIDS, the `split` entity is RECOMMENDED to
+belong to a single recording. In BIDS, the [`split`](../99-appendices/09-entities.md#split) entity is RECOMMENDED to
 deal with split files.
 Please refer to [Appendix VI](../99-appendices/06-meg-file-formats.md) for
 general information on how to deal with such manufacturer specifics and to see
 more examples.
 
-The `proc` label is analogous to `rec` for MR and denotes a variant of a file
+The [`proc-<label>`](../99-appendices/09-entities.md#proc) entity is analogous to [`rec-<label>`](../99-appendices/09-entities.md#proc) for MR and denotes a variant of a file
 that was a result of particular processing performed on the device. This is
 useful for files produced in particular by Elekta’s MaxFilter (e.g. sss, tsss,
 trans, quat, mc, etc.), which some installations impose to be run on raw data
@@ -379,7 +379,7 @@ taped to the skin. Please note that the photos may need to be cropped or blurred
 to conceal identifying features prior to sharing, depending on the terms of the
 consent given by the participant.
 
-The `acq` parameter can be used to indicate acquisition of different photos of
+The [`acq-<label>`](../99-appendices/09-entities.md#acq) entity can be used to indicate acquisition of different photos of
 the same face (or other body part in different angles to show, for example, the
 location of the nasion (NAS) as opposed to the right periauricular point (RPA)).
 
@@ -403,7 +403,7 @@ This file is RECOMMENDED.
 
 The 3-D locations of points that describe the head shape and/or EEG
 electrode locations can be digitized and stored in separate files. The
-`*_acq-<label>` can be used when more than one type of digitization in done for
+[`acq-<label>`](../99-appendices/09-entities.md#acq) entity can be used when more than one type of digitization in done for
 a session, for example when the head points are in a separate file from the EEG
 locations. These files are stored in the specific format of the 3-D digitizer’s
 manufacturer (see [Appendix VI](../99-appendices/06-meg-file-formats.md)).
@@ -429,9 +429,9 @@ In the context of BIDS it is RECOMMENDED to perform an empty-room recording for
 each experimental session.
 It is RECOMMENDED to store the empty-room recording inside a subject folder
 named `sub-emptyroom`.
-The label for the `task-<label>` entity in the empty-room recording SHOULD be
+The label for the [`task-<label>`](../99-appendices/09-entities.md#task) entity in the empty-room recording SHOULD be
 set to `noise`.
-If a `session-<label>` entity is present, its label SHOULD be the date of the
+If a [`session-<label>`](../99-appendices/09-entities.md#ses) entity is present, its label SHOULD be the date of the
 empty-room recording in the format `YYYYMMDD`, i.e., `ses-YYYYMMDD`.
 The `scans.tsv` file containing the date and time of the acquisition SHOULD
 also be included.
diff --git a/src/04-modality-specific-files/03-electroencephalography.md b/src/04-modality-specific-files/03-electroencephalography.md
index 8c42a4fe00..0969533e47 100644
--- a/src/04-modality-specific-files/03-electroencephalography.md
+++ b/src/04-modality-specific-files/03-electroencephalography.md
@@ -315,7 +315,7 @@ REF   -0.0742   -0.0200  -0.0100   cup       Ag/AgCl
 GND   0.0742    -0.0200  -0.0100   cup       Ag/AgCl
 ```
 
-The `acq` parameter can be used to indicate acquisition of the same data. For
+The [`acq-<label>`](../99-appendices/09-entities.md#acq) key/value pair can be used to indicate acquisition of the same data. For
 example, this could be the recording of electrode positions with a different
 electrode position recording device, or repeated digitization before and after
 the recording.
@@ -439,7 +439,7 @@ Please note that the photos may need to be cropped or blurred to conceal
 identifying features prior to sharing, depending on the terms of the consent
 given by the participant.
 
-The `acq` parameter can be used to indicate acquisition of different photos of
+The [`acq-<label>`](../99-appendices/09-entities.md#acq) key/value pair can be used to indicate acquisition of different photos of
 the same face (or other body part in different angles to show, for example, the
 location of the nasion (NAS) as opposed to the right periauricular point (RPA).
 
diff --git a/src/04-modality-specific-files/04-intracranial-electroencephalography.md b/src/04-modality-specific-files/04-intracranial-electroencephalography.md
index ab0603c5aa..a9544bd08d 100644
--- a/src/04-modality-specific-files/04-intracranial-electroencephalography.md
+++ b/src/04-modality-specific-files/04-intracranial-electroencephalography.md
@@ -311,7 +311,7 @@ that coordinates are expected in cartesian coordinates according to the
 `*_coordsystem.json`. If an `*_electrodes.tsv` file is specified, a
 `*_coordsystem.json` file MUST be specified as well.
 
-The optional space label (`*[_space-<label>]_electrodes.tsv`) can be used to
+The optional [`space-<label>`](../99-appendices/09-entities.md#space) entity (`*[_space-<label>]_electrodes.tsv`) can be used to
 indicate the way in which electrode positions are interpreted. The space label
 needs to be taken from the list in
 [Appendix VIII](../99-appendices/08-coordinate-systems.md)
@@ -325,7 +325,7 @@ For examples:
     space)
 
 When referring to the `*_electrodes.tsv` file in a certain _space_ as defined
-above, the `space-<label>` of the accompanying `*_coordsystem.json` MUST
+above, the [`space-<label>`](../99-appendices/09-entities.md#space) of the accompanying `*_coordsystem.json` MUST
 correspond.
 
 For example:
@@ -421,9 +421,9 @@ upper left pixel and (N,0) corresponding to the lower left pixel.
 ### Multiple coordinate systems
 
 If electrode positions are known in multiple coordinate systems (e.g., MRI, CT
-and MNI), these spaces can be distinguished by the optional `[_space-<label>]`
+and MNI), these spaces can be distinguished by the optional [`space-<label>`](../99-appendices/09-entities.md#space)
 field, see the [`*_electrodes.tsv`-section](#electrode-description-_electrodestsv)
-for more information. Note that the `[_space-<label>]` fields must correspond
+for more information. Note that the [`space-<label>`](../99-appendices/09-entities.md#space) fields must correspond
 between `*_electrodes.tsv` and `*_coordsystem.json` if they refer to the same
 data.
 
@@ -458,7 +458,7 @@ during surgery, or screenshots of a brain rendering with electrode positions.
 The photos may need to be cropped and/or blurred to conceal identifying features
 or entirely omitted prior to sharing, depending on obtained consent.
 
-If there are photos of the electrodes, the acquisition field should be specified
+If there are photos of the electrodes, the [`acq-<label>`](../99-appendices/09-entities.md#acq) entity should be specified
 with:
 
 -   `*_photo.jpg` in case of an operative photo
@@ -470,7 +470,7 @@ with:
 
 -   `*_acq-render#_photo.jpg` in case of a rendering
 
-The session label may be used to specify when the photo was taken.
+The [`ses-<label>`](../99-appendices/09-entities.md#ses) entity may be used to specify when the photo was taken.
 
 Example of the operative photo of ECoG electrodes (here is an annotated example in
 which electrodes and vasculature are marked, taken from Hermes et al.,
diff --git a/src/04-modality-specific-files/06-physiological-and-other-continuous-recordings.md b/src/04-modality-specific-files/06-physiological-and-other-continuous-recordings.md
index ec785d768f..f3c3bc7649 100644
--- a/src/04-modality-specific-files/06-physiological-and-other-continuous-recordings.md
+++ b/src/04-modality-specific-files/06-physiological-and-other-continuous-recordings.md
@@ -22,7 +22,7 @@ before the suffix.
 For example for the file `sub-control01_task-nback_run-1_bold.nii.gz`,
 `<matches>` would correspond to `sub-control01_task-nback_run-1`.
 
-The `recording-<label>` entity can be used to distinguish between several
+The [`recording-<label>`](../99-appendices/09-entities.md#recording) entity can be used to distinguish between several
 recording files.
 For example `sub-01_task-bart_recording-eyetracking_physio.tsv.gz` to contain
 the eyetracking data in a certain sampling frequency, and
diff --git a/src/04-modality-specific-files/07-behavioral-experiments.md b/src/04-modality-specific-files/07-behavioral-experiments.md
index 0f2435ac53..d55f17c4de 100644
--- a/src/04-modality-specific-files/07-behavioral-experiments.md
+++ b/src/04-modality-specific-files/07-behavioral-experiments.md
@@ -27,7 +27,7 @@ Additionally, events files that do not include the mandatory `onset` and
 `duration` columns can still be included, but should be labeled `_beh.tsv`
 rather than `_events.tsv`.
 
-The OPTIONAL `acq-<label>` key/value pair corresponds to a custom label to
+The OPTIONAL [`acq-<label>`](../99-appendices/09-entities.md#acq) key/value pair corresponds to a custom label to
 distinguish different conditions present during multiple runs of the same task.
 For example, if a study includes runs of an n-back task, with deep brain
 stimulation turned on or off, the data files may be labelled
diff --git a/src/99-appendices/04-entity-table.md b/src/99-appendices/04-entity-table.md
index 704e6020a9..9f3002bf33 100644
--- a/src/99-appendices/04-entity-table.md
+++ b/src/99-appendices/04-entity-table.md
@@ -1,3 +1,7 @@
+<!--
+  This file is autogenerated based on the src/schema.  DO NOT EDIT DIRECTLY.
+  Follow https://github.com/bids-standard/bids-specification/blob/master/CONTRIBUTING.md#updating-the-schema
+-->
 # Appendix IV: Entity table
 
 This section compiles the entities (key-value pairs) described throughout this
@@ -9,40 +13,41 @@ Entity formats indicate whether the value is alphanumeric
 (`<label>`) or numeric (`<index>`).
 
 A general introduction to entities is given in the section on
-[file name structure](../02-common-principles.md#file-name-structure)
+[file name structure](../02-common-principles.md#file-name-structure),
+while entity definitions are in [Appendix IX](09-entities.md).
 
 ## Magnetic Resonance Imaging
 
-| Entity                                                                                         | Subject       | Session       | Task           | Acquisition   | Contrast Enhancing Agent   | Reconstruction   | Phase-Encoding Direction   | Run           | Corresponding Modality   | Echo           | Recording           |
-|------------------------------------------------------------------------------------------------|---------------|---------------|----------------|---------------|----------------------------|------------------|----------------------------|---------------|--------------------------|----------------|---------------------|
-| Format                                                                                         | `sub-<label>` | `ses-<label>` | `task-<label>` | `acq-<label>` | `ce-<label>`               | `rec-<label>`    | `dir-<label>`              | `run-<index>` | `mod-<label>`            | `echo-<index>` | `recording-<label>` |
-| anat<br>(T1w T2w T1rho T1map T2map T2star FLAIR FLASH PD PDmap PDT2 inplaneT1 inplaneT2 angio) | REQUIRED      | OPTIONAL      |                | OPTIONAL      | OPTIONAL                   | OPTIONAL         |                            | OPTIONAL      |                          |                |                     |
-| anat<br>(defacemask)                                                                           | REQUIRED      | OPTIONAL      |                | OPTIONAL      | OPTIONAL                   | OPTIONAL         |                            | OPTIONAL      | OPTIONAL                 |                |                     |
-| dwi<br>(dwi sbref)                                                                             | REQUIRED      | OPTIONAL      |                | OPTIONAL      |                            |                  | OPTIONAL                   | OPTIONAL      |                          |                |                     |
-| fmap<br>(phasediff phase1 phase2 magnitude1 magnitude2 magnitude fieldmap)                     | REQUIRED      | OPTIONAL      |                | OPTIONAL      |                            |                  |                            | OPTIONAL      |                          |                |                     |
-| fmap<br>(epi)                                                                                  | REQUIRED      | OPTIONAL      |                | OPTIONAL      | OPTIONAL                   |                  | REQUIRED                   | OPTIONAL      |                          |                |                     |
-| func<br>(bold cbv phase sbref events)                                                          | REQUIRED      | OPTIONAL      | REQUIRED       | OPTIONAL      | OPTIONAL                   | OPTIONAL         | OPTIONAL                   | OPTIONAL      |                          | OPTIONAL       |                     |
-| func<br>(physio stim)                                                                          | REQUIRED      | OPTIONAL      | REQUIRED       | OPTIONAL      |                            | OPTIONAL         |                            | OPTIONAL      |                          |                | OPTIONAL            |
+| Entity                                                                                         | Subject                             | Session                             | Task                                  | Acquisition                         | Contrast Enhancing Agent          | Reconstruction                      | Phase-Encoding Direction            | Run                                 | Corresponding Modality              | Echo                                  | Recording                                       |
+|------------------------------------------------------------------------------------------------|-------------------------------------|-------------------------------------|---------------------------------------|-------------------------------------|-----------------------------------|-------------------------------------|-------------------------------------|-------------------------------------|-------------------------------------|---------------------------------------|-------------------------------------------------|
+| Format                                                                                         | [`sub-<label>`](09-entities.md#sub) | [`ses-<label>`](09-entities.md#ses) | [`task-<label>`](09-entities.md#task) | [`acq-<label>`](09-entities.md#acq) | [`ce-<label>`](09-entities.md#ce) | [`rec-<label>`](09-entities.md#rec) | [`dir-<label>`](09-entities.md#dir) | [`run-<index>`](09-entities.md#run) | [`mod-<label>`](09-entities.md#mod) | [`echo-<index>`](09-entities.md#echo) | [`recording-<label>`](09-entities.md#recording) |
+| anat<br>(T1w T2w T1rho T1map T2map T2star FLAIR FLASH PD PDmap PDT2 inplaneT1 inplaneT2 angio) | REQUIRED                            | OPTIONAL                            |                                       | OPTIONAL                            | OPTIONAL                          | OPTIONAL                            |                                     | OPTIONAL                            |                                     |                                       |                                                 |
+| anat<br>(defacemask)                                                                           | REQUIRED                            | OPTIONAL                            |                                       | OPTIONAL                            | OPTIONAL                          | OPTIONAL                            |                                     | OPTIONAL                            | OPTIONAL                            |                                       |                                                 |
+| dwi<br>(dwi sbref)                                                                             | REQUIRED                            | OPTIONAL                            |                                       | OPTIONAL                            |                                   |                                     | OPTIONAL                            | OPTIONAL                            |                                     |                                       |                                                 |
+| fmap<br>(phasediff phase1 phase2 magnitude1 magnitude2 magnitude fieldmap)                     | REQUIRED                            | OPTIONAL                            |                                       | OPTIONAL                            |                                   |                                     |                                     | OPTIONAL                            |                                     |                                       |                                                 |
+| fmap<br>(epi)                                                                                  | REQUIRED                            | OPTIONAL                            |                                       | OPTIONAL                            | OPTIONAL                          |                                     | REQUIRED                            | OPTIONAL                            |                                     |                                       |                                                 |
+| func<br>(bold cbv phase sbref events)                                                          | REQUIRED                            | OPTIONAL                            | REQUIRED                              | OPTIONAL                            | OPTIONAL                          | OPTIONAL                            | OPTIONAL                            | OPTIONAL                            |                                     | OPTIONAL                              |                                                 |
+| func<br>(physio stim)                                                                          | REQUIRED                            | OPTIONAL                            | REQUIRED                              | OPTIONAL                            |                                   | OPTIONAL                            |                                     | OPTIONAL                            |                                     |                                       | OPTIONAL                                        |
 
 ## Encephalography (EEG, iEEG, and MEG)
 
-| Entity                     | Subject       | Session       | Task           | Acquisition   | Run           | Processed (on device)   | Space           | Split           |
-|----------------------------|---------------|---------------|----------------|---------------|---------------|-------------------------|-----------------|-----------------|
-| Format                     | `sub-<label>` | `ses-<label>` | `task-<label>` | `acq-<label>` | `run-<index>` | `proc-<label>`          | `space-<label>` | `split-<index>` |
-| eeg<br>(eeg)               | REQUIRED      | OPTIONAL      | REQUIRED       | OPTIONAL      | OPTIONAL      |                         |                 |                 |
-| ieeg<br>(ieeg)             | REQUIRED      | OPTIONAL      | REQUIRED       | OPTIONAL      | OPTIONAL      |                         |                 |                 |
-| meg<br>(meg)               | REQUIRED      | OPTIONAL      | REQUIRED       | OPTIONAL      | OPTIONAL      | OPTIONAL                |                 | OPTIONAL        |
-| meg<br>(headshape)         | REQUIRED      | OPTIONAL      |                | OPTIONAL      |               |                         | OPTIONAL        |                 |
-| meg<br>(markers)           | REQUIRED      | OPTIONAL      | OPTIONAL       | OPTIONAL      |               |                         | OPTIONAL        |                 |
-| channels<br>(meg eeg ieeg) | REQUIRED      | OPTIONAL      | REQUIRED       |               | OPTIONAL      |                         |                 |                 |
-| electrodes<br>(eeg ieeg)   | REQUIRED      | OPTIONAL      |                | OPTIONAL      |               |                         | OPTIONAL        |                 |
-| events<br>(meg eeg ieeg)   | REQUIRED      | OPTIONAL      | REQUIRED       |               | OPTIONAL      |                         |                 |                 |
-| photo<br>(meg eeg ieeg)    | REQUIRED      | OPTIONAL      |                | OPTIONAL      |               |                         |                 |                 |
+| Entity                     | Subject                             | Session                             | Task                                  | Acquisition                         | Run                                 | Processed (on device)                 | Space                                   | Split                                   |
+|----------------------------|-------------------------------------|-------------------------------------|---------------------------------------|-------------------------------------|-------------------------------------|---------------------------------------|-----------------------------------------|-----------------------------------------|
+| Format                     | [`sub-<label>`](09-entities.md#sub) | [`ses-<label>`](09-entities.md#ses) | [`task-<label>`](09-entities.md#task) | [`acq-<label>`](09-entities.md#acq) | [`run-<index>`](09-entities.md#run) | [`proc-<label>`](09-entities.md#proc) | [`space-<label>`](09-entities.md#space) | [`split-<index>`](09-entities.md#split) |
+| eeg<br>(eeg)               | REQUIRED                            | OPTIONAL                            | REQUIRED                              | OPTIONAL                            | OPTIONAL                            |                                       |                                         |                                         |
+| ieeg<br>(ieeg)             | REQUIRED                            | OPTIONAL                            | REQUIRED                              | OPTIONAL                            | OPTIONAL                            |                                       |                                         |                                         |
+| meg<br>(meg)               | REQUIRED                            | OPTIONAL                            | REQUIRED                              | OPTIONAL                            | OPTIONAL                            | OPTIONAL                              |                                         | OPTIONAL                                |
+| meg<br>(headshape)         | REQUIRED                            | OPTIONAL                            |                                       | OPTIONAL                            |                                     |                                       | OPTIONAL                                |                                         |
+| meg<br>(markers)           | REQUIRED                            | OPTIONAL                            | OPTIONAL                              | OPTIONAL                            |                                     |                                       | OPTIONAL                                |                                         |
+| channels<br>(meg eeg ieeg) | REQUIRED                            | OPTIONAL                            | REQUIRED                              |                                     | OPTIONAL                            |                                       |                                         |                                         |
+| electrodes<br>(eeg ieeg)   | REQUIRED                            | OPTIONAL                            |                                       | OPTIONAL                            |                                     |                                       | OPTIONAL                                |                                         |
+| events<br>(meg eeg ieeg)   | REQUIRED                            | OPTIONAL                            | REQUIRED                              |                                     | OPTIONAL                            |                                       |                                         |                                         |
+| photo<br>(meg eeg ieeg)    | REQUIRED                            | OPTIONAL                            |                                       | OPTIONAL                            |                                     |                                       |                                         |                                         |
 
 ## Behavioral Data
 
-| Entity               | Subject       | Session       | Task           | Acquisition   | Run           | Recording           |
-|----------------------|---------------|---------------|----------------|---------------|---------------|---------------------|
-| Format               | `sub-<label>` | `ses-<label>` | `task-<label>` | `acq-<label>` | `run-<index>` | `recording-<label>` |
-| beh<br>(stim physio) | REQUIRED      | OPTIONAL      | REQUIRED       | OPTIONAL      | OPTIONAL      | OPTIONAL            |
-| beh<br>(events beh)  | REQUIRED      | OPTIONAL      | REQUIRED       | OPTIONAL      | OPTIONAL      |                     |
+| Entity               | Subject                             | Session                             | Task                                  | Acquisition                         | Run                                 | Recording                                       |
+|----------------------|-------------------------------------|-------------------------------------|---------------------------------------|-------------------------------------|-------------------------------------|-------------------------------------------------|
+| Format               | [`sub-<label>`](09-entities.md#sub) | [`ses-<label>`](09-entities.md#ses) | [`task-<label>`](09-entities.md#task) | [`acq-<label>`](09-entities.md#acq) | [`run-<index>`](09-entities.md#run) | [`recording-<label>`](09-entities.md#recording) |
+| beh<br>(stim physio) | REQUIRED                            | OPTIONAL                            | REQUIRED                              | OPTIONAL                            | OPTIONAL                            | OPTIONAL                                        |
+| beh<br>(events beh)  | REQUIRED                            | OPTIONAL                            | REQUIRED                              | OPTIONAL                            | OPTIONAL                            |                                                 |
diff --git a/src/99-appendices/09-entities.md b/src/99-appendices/09-entities.md
new file mode 100644
index 0000000000..4695ccd8b8
--- /dev/null
+++ b/src/99-appendices/09-entities.md
@@ -0,0 +1,193 @@
+<!--
+  This file is autogenerated based on the src/schema.  DO NOT EDIT DIRECTLY.
+  Follow https://github.com/bids-standard/bids-specification/blob/master/CONTRIBUTING.md#updating-the-schema
+-->
+# Appendix IX: Entities
+
+This section compiles the entities (key-value pairs) described throughout this
+specification, and describes each.
+
+A general introduction to entities is given in the section on
+[file name structure](../02-common-principles.md#file-name-structure).
+
+The ordering of entities and whether it is allowed, OPTIONAL, or REQUIRED for
+each is given in the [Entity Table](04-entity-table.md).
+
+## sub
+
+Full name: Subject
+
+Format: `sub-<label>`
+
+Definition: A person or animal participating in the study.
+
+## ses
+
+Full name: Session
+
+Format: `ses-<label>`
+
+Definition: A logical grouping of neuroimaging and behavioral data consistent across
+subjects.
+Session can (but doesn't have to) be synonymous to a visit in a
+longitudinal study.
+In general, subjects will stay in the scanner during one session.
+However, for example, if a subject has to leave the scanner room and then
+be re-positioned on the scanner bed, the set of MRI acquisitions will still
+be considered as a session and match sessions acquired in other subjects.
+Similarly, in situations where different data types are obtained over
+several visits (for example fMRI on one day followed by DWI the day after)
+those can be grouped in one session.
+Defining multiple sessions is appropriate when several identical or similar
+data acquisitions are planned and performed on all -or most- subjects,
+often in the case of some intervention between sessions (e.g., training).
+
+## task
+
+Full name: Task
+
+Format: `task-<label>`
+
+Definition: Each task has a unique label that MUST only consist of letters and/or
+numbers (other characters, including spaces and underscores, are not
+allowed).
+Those labels MUST be consistent across subjects and sessions.
+
+## acq
+
+Full name: Acquisition
+
+Format: `acq-<label>`
+
+Definition: The `acq-<label>` key/value pair corresponds to a custom label the
+user MAY use to distinguish a different set of parameters used for
+acquiring the same modality.
+For example this should be used when a study includes two T1w images - one
+full brain low resolution and and one restricted field of view but high
+resolution.
+In such case two files could have the following names:
+`sub-01_acq-highres_T1w.nii.gz` and `sub-01_acq-lowres_T1w.nii.gz`, however
+the user is free to choose any other label than highres and lowres as long
+as they are consistent across subjects and sessions.
+In case different sequences are used to record the same modality (e.g. RARE
+and FLASH for T1w) this field can also be used to make that distinction.
+At what level of detail to make the distinction (e.g. just between RARE and
+FLASH, or between RARE, FLASH, and FLASHsubsampled) remains at the
+discretion of the researcher.
+
+## ce
+
+Full name: Contrast Enhancing Agent
+
+Format: `ce-<label>`
+
+Definition: The `ce-<label>` key/value can be used to distinguish
+sequences using different contrast enhanced images.
+The label is the name of the contrast agent.
+The key `ContrastBolusIngredient` MAY be also be added in the JSON file,
+with the same label.
+
+## rec
+
+Full name: Reconstruction
+
+Format: `rec-<label>`
+
+Definition: The `rec-<label>` key/value can be used to distinguish
+different reconstruction algorithms (for example ones using motion
+correction).
+
+## dir
+
+Full name: Phase-Encoding Direction
+
+Format: `dir-<label>`
+
+Definition: The `dir-<label>` key/value can be used to distinguish
+different phase-encoding directions.
+
+## run
+
+Full name: Run
+
+Format: `run-<index>`
+
+Definition: If several scans of the same modality are acquired they MUST be indexed
+with a key-value pair: `_run-1`, `_run-2`, ..., `_run-<index>`
+(only nonnegative integers are allowed for the `<index>`).
+When there is only one scan of a given type the run key MAY be omitted.
+
+## mod
+
+Full name: Corresponding Modality
+
+Format: `mod-<label>`
+
+Definition: The `mod-<label>` key/value pair corresponds to modality label for defacing
+masks, e.g., T1w, inplaneT1, referenced by a defacemask image.
+E.g., `sub-01_mod-T1w_defacemask.nii.gz`.
+
+## echo
+
+Full name: Echo
+
+Format: `echo-<index>`
+
+Definition: Multi-echo data MUST be split into one file per echo.
+Each file shares the same name with the exception of the `_echo-<index>`
+key/value.
+Please note that the `<index>` denotes the number/index (in the form of a
+nonnegative integer) of the echo not the echo time value which needs to be
+stored in the field `EchoTime` of the separate JSON file.
+
+## recording
+
+Full name: Recording
+
+Format: `recording-<label>`
+
+Definition: More than one continuous recording file can be included (with different
+sampling frequencies).
+In such case use different labels.
+For example: `_recording-contrast`, `_recording-saturation`.
+
+## proc
+
+Full name: Processed (on device)
+
+Format: `proc-<label>`
+
+Definition: The proc label is analogous to rec for MR and denotes a variant of a file
+that was a result of particular processing performed on the device.
+This is useful for files produced in particular by Elekta’s MaxFilter
+(e.g. sss, tsss, trans, quat, mc, etc.), which some installations impose to
+be run on raw data because of active shielding software corrections before
+the MEG data can actually be exploited.
+
+## space
+
+Full name: Space
+
+Format: `space-<label>`
+
+Definition: The space label (`*[_space-<label>]_electrodes.tsv`) can be used
+to indicate the way in which electrode positions are interpreted.
+The space label needs to be taken from the list in Appendix VIII.
+
+## split
+
+Full name: Split
+
+Format: `split-<index>`
+
+Definition: In the case of long data recordings that exceed a file size of 2Gb, the
+.fif files are conventionally split into multiple parts.
+Each of these files has an internal pointer to the next file.
+This is important when renaming these split recordings to the BIDS
+convention.
+
+Instead of a simple renaming, files should be read in and saved under their
+new names with dedicated tools like MNE, which will ensure that not only
+the file names, but also the internal file pointers will be updated.
+It is RECOMMENDED that .fif files with multiple parts use the
+`split-<index>` entity to indicate each part.
diff --git a/src/schema/entities.yaml b/src/schema/entities.yaml
index 10cf4cfbe7..f1b6d1c6c1 100644
--- a/src/schema/entities.yaml
+++ b/src/schema/entities.yaml
@@ -33,16 +33,16 @@ task:
 acq:
   name: Acquisition
   description: |
-    The OPTIONAL acq-<label> key/value pair corresponds to a custom label the
+    The `acq-<label>` key/value pair corresponds to a custom label the
     user MAY use to distinguish a different set of parameters used for
     acquiring the same modality.
     For example this should be used when a study includes two T1w images - one
     full brain low resolution and and one restricted field of view but high
     resolution.
     In such case two files could have the following names:
-    sub-01_acq-highres_T1w.nii.gz and sub-01_acq-lowres_T1w.nii.gz, however the
-    user is free to choose any other label than highres and lowres as long as
-    they are consistent across subjects and sessions.
+    `sub-01_acq-highres_T1w.nii.gz` and `sub-01_acq-lowres_T1w.nii.gz`, however
+    the user is free to choose any other label than highres and lowres as long
+    as they are consistent across subjects and sessions.
     In case different sequences are used to record the same modality (e.g. RARE
     and FLASH for T1w) this field can also be used to make that distinction.
     At what level of detail to make the distinction (e.g. just between RARE and
@@ -52,23 +52,23 @@ acq:
 ce:
   name: Contrast Enhancing Agent
   description: |
-    Similarly the OPTIONAL ce-<label> key/value can be used to distinguish
+    The `ce-<label>` key/value can be used to distinguish
     sequences using different contrast enhanced images.
     The label is the name of the contrast agent.
-    The key ContrastBolusIngredient MAY be also be added in the JSON file, with
-    the same label.
+    The key `ContrastBolusIngredient` MAY be also be added in the JSON file,
+    with the same label.
   format: label
 rec:
   name: Reconstruction
   description: |
-    Similarly the OPTIONAL rec-<label> key/value can be used to distinguish
+    The `rec-<label>` key/value can be used to distinguish
     different reconstruction algorithms (for example ones using motion
     correction).
   format: label
 dir:
   name: Phase-Encoding Direction
   description: |
-    Similarly the OPTIONAL dir-<label> key/value can be used to distinguish
+    The `dir-<label>` key/value can be used to distinguish
     different phase-encoding directions.
   format: label
 run:
@@ -82,9 +82,9 @@ run:
 mod:
   name: Corresponding Modality
   description: |
-    In such cases the OPTIONAL `mod-<label>` key/value pair corresponds to
-    modality label for eg: T1w, inplaneT1, referenced by a defacemask image.
-    E.g., sub-01_mod-T1w_defacemask.nii.gz.
+    The `mod-<label>` key/value pair corresponds to modality label for defacing
+    masks, e.g., T1w, inplaneT1, referenced by a defacemask image.
+    E.g., `sub-01_mod-T1w_defacemask.nii.gz`.
   format: label
 echo:
   name: Echo
@@ -117,7 +117,7 @@ proc:
 space:
   name: Space
   description: |
-    The optional space label (`*[_space-<label>]_electrodes.tsv`) can be used
+    The space label (`*[_space-<label>]_electrodes.tsv`) can be used
     to indicate the way in which electrode positions are interpreted.
     The space label needs to be taken from the list in Appendix VIII.
   format: label
@@ -129,6 +129,7 @@ split:
     Each of these files has an internal pointer to the next file.
     This is important when renaming these split recordings to the BIDS
     convention.
+
     Instead of a simple renaming, files should be read in and saved under their
     new names with dedicated tools like MNE, which will ensure that not only
     the file names, but also the internal file pointers will be updated.
diff --git a/tools/bids_schema.py b/tools/bids_schema.py
index ce17feb9ed..e85be97668 100755
--- a/tools/bids_schema.py
+++ b/tools/bids_schema.py
@@ -109,18 +109,44 @@ def _get_parser():
         type=Path,
         help=('Path to schema to show.')
     )
-    # entity_table()
-    entity_parser = subparsers.add_parser(
-        'entity',
-        help=('Print entity table')
+    # save_entity_table()
+    entitytable_parser = subparsers.add_parser(
+        'entitytable',
+        help=('Save entity table to file')
     )
-    entity_parser.set_defaults(func=save_entity_table)
-    entity_parser.add_argument(
+    entitytable_parser.set_defaults(func=save_entity_table)
+    entitytable_parser.add_argument(
         'schema_path',
         type=Path,
         help=('Path to schema to show.')
     )
-    entity_parser.add_argument(
+    entitytable_parser.add_argument(
+        'out_file',
+        type=str,
+        help=('Output filename.')
+    )
+    entitytable_parser.add_argument(
+        '--entities_file',
+        type=str,
+        help=('File in which entities are described. '
+              'This is used for hyperlinks in the table, so the path to the '
+              'file should be considered from the location of out_file. '
+              'Default is "09-entities.md".'),
+        default='09-entities.md',
+        required=False,
+    )
+    # save_entities()
+    entities_parser = subparsers.add_parser(
+        'entities',
+        help=('Save entities to file')
+    )
+    entities_parser.set_defaults(func=save_entities)
+    entities_parser.add_argument(
+        'schema_path',
+        type=Path,
+        help=('Path to schema to show.')
+    )
+    entities_parser.add_argument(
         'out_file',
         type=str,
         help=('Output filename.')
@@ -168,12 +194,55 @@ def show(schema_path):
     print(yaml.safe_dump(schema, default_flow_style=False))
 
 
+def save_entities(schema_path, out_file):
+    """Save entity definitions to a markdown file.
+    Each entity gets its own heading.
+    """
+    schema = load_schema(schema_path)
+    entities = schema['entities']
+    intro_text = """\
+<!--
+  This file is autogenerated based on the src/schema.  DO NOT EDIT DIRECTLY.
+  Follow https://github.com/bids-standard/bids-specification/blob/master/CONTRIBUTING.md#updating-the-schema
+-->
+# Appendix IX: Entities
+
+This section compiles the entities (key-value pairs) described throughout this
+specification, and describes each.
+
+A general introduction to entities is given in the section on
+[file name structure](../02-common-principles.md#file-name-structure).
+
+The ordering of entities and whether it is allowed, OPTIONAL, or REQUIRED for
+each is given in the [Entity Table](04-entity-table.md).
+"""
+    with open(out_file, 'w') as fo:
+        fo.write(intro_text)
+        for entity, entity_info in entities.items():
+            fo.write('\n')
+            fo.write('## {}'.format(entity))
+            fo.write('\n\n')
+            fo.write('Full name: {}'.format(entity_info['name']))
+            fo.write('\n\n')
+            fo.write('Format: `{}-<{}>`'.format(entity, entity_info['format']))
+            fo.write('\n\n')
+            fo.write('Definition: {}'.format(entity_info['description']))
+
+
 def drop_unused_entities(df):
+    """Remove columns from a dataframe where all values in the column are NaNs.
+    For entity tables, this limits each table to only entities thare are used
+    within the modality.
+    """
     df = df.replace('', np.nan).dropna(axis=1, how='all').fillna('')
     return df
 
 
 def flatten_multiindexed_columns(df):
+    """Remove multi-indexing of multi-indexed column headers.
+    The first layer is the "DataType", while the second layer is the "Format".
+    This second layer will become a new row.
+    """
     # Flatten multi-index
     vals = df.index.tolist()
     df.loc['Format'] = df.columns.get_level_values(1)
@@ -184,7 +253,7 @@ def flatten_multiindexed_columns(df):
     return df
 
 
-def make_entity_table(schema_path):
+def make_entity_table(schema_path, entities_file='09-entities.md'):
     """Produce entity table (markdown) based on schema.
     This only works if the top-level schema *directory* is provided.
 
@@ -192,11 +261,16 @@ def make_entity_table(schema_path):
     ----------
     schema_path : str
         Folder containing schema, which is stored in yaml files.
+    entities_file : str, optional
+        File in which entities are described.
+        This is used for hyperlinks in the table, so the path to the file
+        should be considered from the location of out_file.
+        Default is '09-entities.md'.
 
     Returns
     -------
     table : pandas.DataFrame
-        DataFrame of entity table, with two layers of columns.
+        DataFrame of entity table, with two layers of column headers.
     """
     schema = load_schema(schema_path)
 
@@ -210,7 +284,8 @@ def make_entity_table(schema_path):
     # Compose header and formats first
     for i, (entity, spec) in enumerate(schema['entities'].items()):
         header.append(spec["name"])
-        formats.append(f'`{entity}-<{spec["format"]}>`')
+        formats.append(f'[`{entity}-<{spec["format"]}>`]'
+                       f'({entities_file}#{entity})')
         entity_to_col[entity] = i + 1
 
     # Go through data types
@@ -258,9 +333,10 @@ def make_entity_table(schema_path):
     return table
 
 
-def make_entity_table_markdown(schema_path, tablefmt='github'):
+def make_entity_table_markdown(schema_path, tablefmt='github',
+                               entities_file='09-entities.md'):
     """
-    Create a tabulated entity table from the schema.
+    Create a group of tabulated entity tables from the schema.
 
     This only works if the top-level schema *directory* is provided.
 
@@ -270,6 +346,11 @@ def make_entity_table_markdown(schema_path, tablefmt='github'):
         Path to schema.
     tablefmt : {'github'}, optional
         Format for tabulated table.
+    entities_file : str, optional
+        File in which entities are described.
+        This is used for hyperlinks in the table, so the path to the file
+        should be considered from the location of out_file.
+        Default is '09-entities.md'.
 
     Returns
     -------
@@ -277,7 +358,7 @@ def make_entity_table_markdown(schema_path, tablefmt='github'):
         Dictionary of tabulated entity tables, with table title as key.
     """
     from tabulate import tabulate
-    table = make_entity_table(schema_path)
+    table = make_entity_table(schema_path, entities_file=entities_file)
 
     # Split table
     EG_DATATYPES = ['eeg', 'ieeg', 'meg', 'channels', 'electrodes', 'events',
@@ -311,11 +392,31 @@ def make_entity_table_markdown(schema_path, tablefmt='github'):
     return out_tables
 
 
-def save_entity_table(schema_path, out_file):
+def save_entity_table(schema_path, out_file, entities_file='09-entities.md'):
+    """
+    Create entity table from schema path and then save the table to a markdown
+    file.
 
+    Parameters
+    ----------
+    schema_path : str
+        Path to folder containing schema.
+        Do not point to a specific file in the schema.
+    out_file : str
+        Output file for the entity table.
+    entities_file : str, optional
+        File in which entities are described.
+        This is used for hyperlinks in the table, so the path to the file
+        should be considered from the location of out_file.
+        Default is '09-entities.md'.
+    """
     tables = make_entity_table_markdown(schema_path)
 
     intro_text = """\
+<!--
+  This file is autogenerated based on the src/schema.  DO NOT EDIT DIRECTLY.
+  Follow https://github.com/bids-standard/bids-specification/blob/master/CONTRIBUTING.md#updating-the-schema
+-->
 # Appendix IV: Entity table
 
 This section compiles the entities (key-value pairs) described throughout this
@@ -327,8 +428,10 @@ def save_entity_table(schema_path, out_file):
 (`<label>`) or numeric (`<index>`).
 
 A general introduction to entities is given in the section on
-[file name structure](../02-common-principles.md#file-name-structure)
-"""
+[file name structure](../02-common-principles.md#file-name-structure),
+while entity definitions are in [Appendix IX]({entities_file}).
+""".format(entities_file=entities_file)
+
     with open(out_file, 'w') as fo:
         fo.write(intro_text)
         fo.write('\n')
@@ -347,8 +450,11 @@ def _main(argv=None):
 
     Examples
     --------
-    >>> python bids_schema.py entity ../src/schema/ \
+    >>> python bids_schema.py entitytable ../src/schema/ \
     >>> ../src/99-appendices/04-entity-table.md
+
+    >>> python bids_schema.py entities ../src/schema/ \
+    >>> ../src/99-appendices/09-entities.md
     """
     options = _get_parser().parse_args(argv)
     args = vars(options).copy()