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This work aims at providing fundamental general tools for the analysis of water spectra as observed in protoplanetary disks with JWST-MIRI. We analyze 25 high-quality spectra from the JDISC Survey reduced with asteroid calibrators as presented in Pontoppidan et al. 2024. First, we present a spectral atlas to illustrate the clustering of water transitions from different upper level energies ($E_u$) and identify single (un-blended) lines that provide the most reliable measurements. With the atlas, we demonstrate two important excitation effects: one related to the opacity saturation of ortho-para line pairs that overlap, and the other to the sub-thermal excitation of $v=1-1$ lines scattered across the $v=0-0$ rotational band. Second, from this larger line selection we define a list of fundamental lines spanning $E_u$ from 1500 to 6000 K to develop simple line-ratio diagrams as diagnostics of temperature components and column density. Third, we report the detection of disk-rotation Doppler broadening of molecular lines, which demonstrates the radial distribution of water emission at different $E_u$ and confirms from gas kinematics a radially-extended $\approx 170$--220 K reservoir, close to the ice sublimation front. We also report the detection of narrow blue-shifted absorption from an inner disk wind in ro-vibrational H2O and CO lines, which may be observed in disks at inclinations $> 50$ deg. We summarize these findings and tools into a general recipe that should be beneficial to community efforts to study water in planet-forming regions., Comment: Community input and feedback is very welcome. Referee report received and asking for minor revisions. Some analysis updates are in progress. The rest of the sample in Appendix H will be included later

We present MIRI MRS observations of the large, multi-gapped protoplanetary disk around the T-Tauri star AS 209. The observations reveal hundreds of water vapor lines from 4.9 to 25.5 $\mu$m towards the inner $\sim1$ au in the disk, including the first detection of ro-vibrational water emission in this disk. The spectrum is dominated by hot ($\sim800$ K) water vapor and OH gas, with only marginal detections of CO$_2$, HCN, and a possible colder water vapor component. Using slab models with a detailed treatment of opacities and line overlap, we retrieve the column density, emitting area, and excitation temperature of water vapor and OH, and provide upper limits for the observable mass of other molecules. Compared to MIRI spectra of other T-Tauri disks, the inner disk of AS 209 does not appear to be atypically depleted in CO$_2$ nor HCN. Based on \textit{Spitzer IRS} observations, we further find evidence for molecular emission variability over a 10-year baseline. Water, OH, and CO$_2$ line luminosities have decreased by factors 2-4 in the new MIRI epoch, yet there are minimal continuum emission variations. The origin of this variability is yet to be understood., Comment: Accepted for publication in ApJ